Starting phenix.real_space_refine on Tue Aug 4 22:39:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdr_60006/08_2026/8zdr_60006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdr_60006/08_2026/8zdr_60006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zdr_60006/08_2026/8zdr_60006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdr_60006/08_2026/8zdr_60006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zdr_60006/08_2026/8zdr_60006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdr_60006/08_2026/8zdr_60006.map" } resolution = 2.65 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= -0.001 sd= 0.065 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 187 5.49 5 S 16 5.16 5 C 3966 2.51 5 N 1357 2.21 5 O 1913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7440 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3062 Classifications: {'RNA': 144} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 68, 'rna3p_pyr': 66} Link IDs: {'rna2p': 10, 'rna3p': 133} Chain breaks: 2 Chain: "B" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 651 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3497 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 12, 'TRANS': 433} Chain breaks: 12 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 5, 'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4788 SG CYS C 182 32.132 35.295 88.845 1.00 40.09 S ATOM 4823 SG CYS C 187 28.882 36.876 90.200 1.00 51.66 S ATOM 5426 SG CYS C 264 32.260 38.220 91.318 1.00 39.17 S Time building chain proxies: 1.79, per 1000 atoms: 0.24 Number of scatterers: 7440 At special positions: 0 Unit cell: (74.7, 97.11, 118.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 16 16.00 P 187 15.00 O 1913 8.00 N 1357 7.00 C 3966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 289.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" ND1 HIS C 267 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 187 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 182 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 264 " Number of angles added : 3 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 5 sheets defined 47.5% alpha, 7.6% beta 67 base pairs and 122 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'C' and resid 39 through 74 removed outlier: 3.597A pdb=" N ARG C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 136 through 151 Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 197 through 207 removed outlier: 3.514A pdb=" N ILE C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 229 through 239 removed outlier: 3.509A pdb=" N LYS C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 264 through 275 removed outlier: 3.871A pdb=" N ILE C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU C 269 " --> pdb=" O GLU C 266 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 271 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 272 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 302 Processing helix chain 'C' and resid 451 through 460 removed outlier: 3.726A pdb=" N ARG C 460 " --> pdb=" O ARG C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 removed outlier: 3.552A pdb=" N ASP C 500 " --> pdb=" O HIS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 575 No H-bonds generated for 'chain 'C' and resid 573 through 575' Processing helix chain 'C' and resid 579 through 583 Processing helix chain 'C' and resid 585 through 600 removed outlier: 3.911A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 616 Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.968A pdb=" N ASN C 32 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 560 through 562 Processing sheet with id=AA3, first strand: chain 'C' and resid 640 through 643 Processing sheet with id=AA4, first strand: chain 'C' and resid 672 through 673 removed outlier: 3.900A pdb=" N GLY C 656 " --> pdb=" O ARG C 672 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 721 through 722 removed outlier: 4.164A pdb=" N VAL C 735 " --> pdb=" O ILE C 722 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 166 hydrogen bonds 296 hydrogen bond angles 0 basepair planarities 67 basepair parallelities 122 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 792 1.30 - 1.43: 3109 1.43 - 1.56: 3642 1.56 - 1.68: 372 1.68 - 1.81: 25 Bond restraints: 7940 Sorted by residual: bond pdb=" C GLU C 586 " pdb=" N THR C 587 " ideal model delta sigma weight residual 1.334 1.238 0.096 1.33e-02 5.65e+03 5.23e+01 bond pdb=" C LYS C 597 " pdb=" N ARG C 598 " ideal model delta sigma weight residual 1.332 1.421 -0.089 1.35e-02 5.49e+03 4.39e+01 bond pdb=" C SER C 585 " pdb=" N GLU C 586 " ideal model delta sigma weight residual 1.335 1.424 -0.089 1.36e-02 5.41e+03 4.29e+01 bond pdb=" C PHE C 599 " pdb=" N ASP C 600 " ideal model delta sigma weight residual 1.333 1.241 0.092 1.45e-02 4.76e+03 4.00e+01 bond pdb=" C LYS C 247 " pdb=" O LYS C 247 " ideal model delta sigma weight residual 1.236 1.173 0.064 1.15e-02 7.56e+03 3.06e+01 ... (remaining 7935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 11067 1.98 - 3.96: 475 3.96 - 5.94: 20 5.94 - 7.92: 2 7.92 - 9.90: 2 Bond angle restraints: 11566 Sorted by residual: angle pdb=" CA PHE C 599 " pdb=" C PHE C 599 " pdb=" N ASP C 600 " ideal model delta sigma weight residual 117.82 124.77 -6.95 1.42e+00 4.96e-01 2.39e+01 angle pdb=" C1' U A 95 " pdb=" N1 U A 95 " pdb=" C2 U A 95 " ideal model delta sigma weight residual 117.70 123.53 -5.83 1.20e+00 6.94e-01 2.36e+01 angle pdb=" O4' DG B 3 " pdb=" C4' DG B 3 " pdb=" C3' DG B 3 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" O SER C 585 " pdb=" C SER C 585 " pdb=" N GLU C 586 " ideal model delta sigma weight residual 122.93 128.78 -5.85 1.23e+00 6.61e-01 2.26e+01 angle pdb=" O PHE C 599 " pdb=" C PHE C 599 " pdb=" N ASP C 600 " ideal model delta sigma weight residual 122.33 116.04 6.29 1.34e+00 5.57e-01 2.21e+01 ... (remaining 11561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 4356 35.22 - 70.44: 502 70.44 - 105.66: 41 105.66 - 140.88: 2 140.88 - 176.10: 6 Dihedral angle restraints: 4907 sinusoidal: 3617 harmonic: 1290 Sorted by residual: dihedral pdb=" O4' U A 94 " pdb=" C1' U A 94 " pdb=" N1 U A 94 " pdb=" C2 U A 94 " ideal model delta sinusoidal sigma weight residual -128.00 31.96 -159.96 1 1.70e+01 3.46e-03 6.44e+01 dihedral pdb=" O4' U A 95 " pdb=" C1' U A 95 " pdb=" N1 U A 95 " pdb=" C2 U A 95 " ideal model delta sinusoidal sigma weight residual 232.00 121.50 110.50 1 1.70e+01 3.46e-03 4.48e+01 dihedral pdb=" O4' U A 68 " pdb=" C1' U A 68 " pdb=" N1 U A 68 " pdb=" C2 U A 68 " ideal model delta sinusoidal sigma weight residual -128.00 -66.98 -61.02 1 1.70e+01 3.46e-03 1.71e+01 ... (remaining 4904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1030 0.045 - 0.090: 186 0.090 - 0.134: 178 0.134 - 0.179: 29 0.179 - 0.224: 7 Chirality restraints: 1430 Sorted by residual: chirality pdb=" C1' G A 14 " pdb=" O4' G A 14 " pdb=" C2' G A 14 " pdb=" N9 G A 14 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C3' DG B 3 " pdb=" C4' DG B 3 " pdb=" O3' DG B 3 " pdb=" C2' DG B 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" C3' DG B 8 " pdb=" C4' DG B 8 " pdb=" O3' DG B 8 " pdb=" C2' DG B 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 1427 not shown) Planarity restraints: 793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 636 " 0.064 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO C 637 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 637 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 637 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 597 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C LYS C 597 " -0.068 2.00e-02 2.50e+03 pdb=" O LYS C 597 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG C 598 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 14 " 0.026 2.00e-02 2.50e+03 1.20e-02 4.30e+00 pdb=" N9 G A 14 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G A 14 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 14 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 14 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 14 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 14 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G A 14 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A 14 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 14 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 14 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 14 " 0.000 2.00e-02 2.50e+03 ... (remaining 790 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 37 2.50 - 3.10: 5119 3.10 - 3.70: 13988 3.70 - 4.30: 20346 4.30 - 4.90: 27345 Nonbonded interactions: 66835 Sorted by model distance: nonbonded pdb=" O6 G A 90 " pdb=" O2 U A 104 " model vdw 1.902 2.432 nonbonded pdb=" OE2 GLU C 723 " pdb=" N THR C 734 " model vdw 2.062 3.120 nonbonded pdb=" N GLU C 270 " pdb=" OE1 GLU C 270 " model vdw 2.135 3.120 nonbonded pdb=" O ASN C 77 " pdb=" OG1 THR C 80 " model vdw 2.182 3.040 nonbonded pdb=" OP1 U A 51 " pdb=" NZ LYS C 629 " model vdw 2.210 3.120 ... (remaining 66830 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: 1.960 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.940 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.006 0.096 7944 Z= 0.464 Angle : 0.802 9.899 11569 Z= 0.660 Chirality : 0.053 0.224 1430 Planarity : 0.006 0.098 793 Dihedral : 23.334 176.103 4061 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.55 % Allowed : 13.70 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.40), residues: 420 helix: 0.20 (0.37), residues: 180 sheet: 0.48 (1.33), residues: 10 loop : -0.78 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 47 TYR 0.014 0.002 TYR C 70 PHE 0.025 0.002 PHE C 596 TRP 0.006 0.003 TRP C 452 HIS 0.002 0.001 HIS C 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.46 ( 7940) covalent geometry : angle 0.80169 / 0.66 (11566) hydrogen bonds : bond 0.11473 / 11.78 ( 324) hydrogen bonds : angle 4.61892 / 6.52 ( 728) metal coordination : bond 0.00486 / 0.31 ( 4) metal coordination : angle 1.10530 / 1.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7285 (mt0) cc_final: 0.6472 (tp-100) REVERT: C 739 LYS cc_start: 0.5943 (mmmt) cc_final: 0.5666 (mtmm) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.5294 time to fit residues: 24.3200 Evaluate side-chains 37 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 248 GLN C 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.193143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147958 restraints weight = 6856.503| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.95 r_work: 0.3719 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7944 Z= 0.186 Angle : 0.631 7.933 11569 Z= 0.368 Chirality : 0.045 0.344 1430 Planarity : 0.006 0.061 793 Dihedral : 24.272 167.584 3191 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.74 % Allowed : 13.70 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.39), residues: 420 helix: 0.43 (0.37), residues: 175 sheet: -0.16 (1.27), residues: 10 loop : -0.66 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 283 TYR 0.014 0.002 TYR C 169 PHE 0.014 0.002 PHE C 596 TRP 0.007 0.002 TRP C 452 HIS 0.006 0.002 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.19 ( 7940) covalent geometry : angle 0.63044 / 0.37 (11566) hydrogen bonds : bond 0.07060 / 7.42 ( 324) hydrogen bonds : angle 3.37124 / 4.32 ( 728) metal coordination : bond 0.01293 / 0.83 ( 4) metal coordination : angle 1.75499 / 3.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7262 (mt0) cc_final: 0.6113 (tp-100) REVERT: C 79 SER cc_start: 0.8287 (p) cc_final: 0.8037 (m) REVERT: C 239 HIS cc_start: 0.4397 (OUTLIER) cc_final: 0.4162 (m90) REVERT: C 247 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7092 (ttpt) REVERT: C 739 LYS cc_start: 0.5600 (mmmt) cc_final: 0.5113 (mtmm) outliers start: 10 outliers final: 3 residues processed: 44 average time/residue: 0.5423 time to fit residues: 25.4357 Evaluate side-chains 42 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 0.0770 chunk 1 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7838 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.194948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150158 restraints weight = 6864.087| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 0.95 r_work: 0.3744 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7944 Z= 0.147 Angle : 0.554 7.902 11569 Z= 0.331 Chirality : 0.040 0.337 1430 Planarity : 0.004 0.045 793 Dihedral : 24.135 170.340 3191 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.74 % Allowed : 14.79 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.40), residues: 420 helix: 0.80 (0.38), residues: 177 sheet: -0.08 (1.34), residues: 10 loop : -0.62 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 63 TYR 0.011 0.001 TYR C 169 PHE 0.007 0.001 PHE C 648 TRP 0.002 0.001 TRP C 452 HIS 0.007 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 ( 7940) covalent geometry : angle 0.55352 / 0.33 (11566) hydrogen bonds : bond 0.05849 / 6.13 ( 324) hydrogen bonds : angle 3.12962 / 3.98 ( 728) metal coordination : bond 0.00670 / 0.44 ( 4) metal coordination : angle 1.32140 / 2.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7237 (mt0) cc_final: 0.6085 (tp-100) REVERT: C 79 SER cc_start: 0.8338 (p) cc_final: 0.8092 (m) REVERT: C 247 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7174 (ttpt) REVERT: C 621 LYS cc_start: 0.5862 (OUTLIER) cc_final: 0.5653 (ptpp) outliers start: 10 outliers final: 4 residues processed: 47 average time/residue: 0.5069 time to fit residues: 25.3995 Evaluate side-chains 45 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 614 GLU Chi-restraints excluded: chain C residue 621 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.191194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145936 restraints weight = 6907.263| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 0.95 r_work: 0.3697 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7944 Z= 0.194 Angle : 0.617 8.180 11569 Z= 0.354 Chirality : 0.044 0.346 1430 Planarity : 0.005 0.041 793 Dihedral : 24.069 171.441 3191 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.56 % Allowed : 14.79 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.39), residues: 420 helix: 0.66 (0.38), residues: 177 sheet: -0.10 (1.27), residues: 10 loop : -0.74 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 137 TYR 0.012 0.002 TYR C 169 PHE 0.010 0.002 PHE C 83 TRP 0.003 0.001 TRP C 452 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.19 ( 7940) covalent geometry : angle 0.61673 / 0.35 (11566) hydrogen bonds : bond 0.06994 / 7.25 ( 324) hydrogen bonds : angle 3.12477 / 3.99 ( 728) metal coordination : bond 0.01574 / 0.98 ( 4) metal coordination : angle 1.45910 / 2.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7288 (mt0) cc_final: 0.6105 (tp-100) REVERT: C 79 SER cc_start: 0.8398 (p) cc_final: 0.8162 (m) REVERT: C 247 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7183 (ttpt) REVERT: C 696 LEU cc_start: 0.7454 (mp) cc_final: 0.7199 (tp) REVERT: C 739 LYS cc_start: 0.5474 (mmmt) cc_final: 0.4811 (ptpt) outliers start: 13 outliers final: 7 residues processed: 49 average time/residue: 0.5114 time to fit residues: 26.7570 Evaluate side-chains 45 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.193904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149249 restraints weight = 6926.865| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 0.95 r_work: 0.3737 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7944 Z= 0.144 Angle : 0.541 8.132 11569 Z= 0.322 Chirality : 0.039 0.337 1430 Planarity : 0.004 0.035 793 Dihedral : 23.989 172.482 3191 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.47 % Allowed : 16.99 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.40), residues: 420 helix: 1.01 (0.39), residues: 177 sheet: -0.06 (1.36), residues: 10 loop : -0.68 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.010 0.001 TYR C 169 PHE 0.006 0.001 PHE C 648 TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 ( 7940) covalent geometry : angle 0.54021 / 0.32 (11566) hydrogen bonds : bond 0.05781 / 6.00 ( 324) hydrogen bonds : angle 3.01661 / 3.85 ( 728) metal coordination : bond 0.00880 / 0.56 ( 4) metal coordination : angle 1.35269 / 2.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7254 (mt0) cc_final: 0.6113 (tp-100) REVERT: C 79 SER cc_start: 0.8345 (p) cc_final: 0.8125 (m) REVERT: C 247 LYS cc_start: 0.7731 (ttmt) cc_final: 0.7213 (ttpt) REVERT: C 580 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7016 (pt0) REVERT: C 621 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5707 (ptpp) REVERT: C 739 LYS cc_start: 0.5399 (mmmt) cc_final: 0.4808 (ptpt) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.5878 time to fit residues: 29.8692 Evaluate side-chains 46 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 614 GLU Chi-restraints excluded: chain C residue 621 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.192131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147006 restraints weight = 6886.765| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 0.94 r_work: 0.3705 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7944 Z= 0.176 Angle : 0.576 8.447 11569 Z= 0.336 Chirality : 0.041 0.344 1430 Planarity : 0.005 0.049 793 Dihedral : 23.925 172.470 3191 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.11 % Allowed : 15.89 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.39), residues: 420 helix: 0.89 (0.38), residues: 177 sheet: -0.01 (1.35), residues: 10 loop : -0.75 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 556 TYR 0.011 0.002 TYR C 169 PHE 0.009 0.001 PHE C 83 TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.18 ( 7940) covalent geometry : angle 0.57599 / 0.34 (11566) hydrogen bonds : bond 0.06445 / 6.72 ( 324) hydrogen bonds : angle 3.09499 / 4.02 ( 728) metal coordination : bond 0.01408 / 0.88 ( 4) metal coordination : angle 1.52105 / 2.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7313 (mt0) cc_final: 0.6120 (tp-100) REVERT: C 247 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7091 (tttt) REVERT: C 580 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7215 (pt0) outliers start: 15 outliers final: 10 residues processed: 49 average time/residue: 0.4940 time to fit residues: 25.8365 Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 614 GLU Chi-restraints excluded: chain C residue 621 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 40 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.192862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147912 restraints weight = 6899.350| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 0.95 r_work: 0.3718 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7944 Z= 0.165 Angle : 0.562 8.839 11569 Z= 0.330 Chirality : 0.040 0.338 1430 Planarity : 0.005 0.047 793 Dihedral : 23.862 173.017 3191 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.29 % Allowed : 17.53 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.00 (0.39), residues: 420 helix: 1.00 (0.38), residues: 177 sheet: -0.06 (1.33), residues: 10 loop : -0.78 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 556 TYR 0.010 0.002 TYR C 169 PHE 0.008 0.001 PHE C 83 TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.17 ( 7940) covalent geometry : angle 0.56131 / 0.33 (11566) hydrogen bonds : bond 0.06024 / 6.26 ( 324) hydrogen bonds : angle 3.02515 / 3.89 ( 728) metal coordination : bond 0.01238 / 0.78 ( 4) metal coordination : angle 1.53026 / 2.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7305 (mt0) cc_final: 0.6122 (tp-100) REVERT: C 247 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7263 (ttpt) REVERT: C 461 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5308 (tm-30) REVERT: C 580 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7217 (pt0) REVERT: C 739 LYS cc_start: 0.5679 (mmmt) cc_final: 0.4864 (ptpt) outliers start: 12 outliers final: 8 residues processed: 47 average time/residue: 0.5414 time to fit residues: 27.0990 Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 17 optimal weight: 0.0870 chunk 6 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 651 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.193674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.148747 restraints weight = 6925.835| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 0.95 r_work: 0.3727 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7944 Z= 0.153 Angle : 0.547 9.777 11569 Z= 0.322 Chirality : 0.039 0.336 1430 Planarity : 0.005 0.066 793 Dihedral : 23.757 172.945 3191 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.74 % Allowed : 17.26 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.40), residues: 420 helix: 1.18 (0.38), residues: 177 sheet: -0.09 (1.35), residues: 10 loop : -0.75 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 65 TYR 0.010 0.001 TYR C 169 PHE 0.007 0.001 PHE C 83 TRP 0.003 0.001 TRP C 452 HIS 0.002 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 ( 7940) covalent geometry : angle 0.54670 / 0.32 (11566) hydrogen bonds : bond 0.05716 / 6.00 ( 324) hydrogen bonds : angle 2.98118 / 3.85 ( 728) metal coordination : bond 0.01087 / 0.68 ( 4) metal coordination : angle 1.39158 / 2.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.218 Fit side-chains REVERT: C 46 ASP cc_start: 0.7111 (m-30) cc_final: 0.6870 (m-30) REVERT: C 58 GLN cc_start: 0.7283 (mt0) cc_final: 0.6104 (tp-100) REVERT: C 247 LYS cc_start: 0.7797 (ttmt) cc_final: 0.7251 (ttpt) REVERT: C 263 PHE cc_start: 0.7460 (m-80) cc_final: 0.7182 (m-80) REVERT: C 461 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5256 (tm-30) REVERT: C 580 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7230 (pt0) REVERT: C 739 LYS cc_start: 0.5346 (mmmt) cc_final: 0.4580 (ptpt) outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.4639 time to fit residues: 21.8011 Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.190649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145560 restraints weight = 6807.016| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 0.93 r_work: 0.3690 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7944 Z= 0.202 Angle : 0.608 7.030 11569 Z= 0.349 Chirality : 0.044 0.343 1430 Planarity : 0.006 0.080 793 Dihedral : 23.771 172.103 3191 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.56 % Allowed : 17.53 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.39), residues: 420 helix: 0.86 (0.38), residues: 177 sheet: -0.01 (1.33), residues: 10 loop : -0.81 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 556 TYR 0.012 0.002 TYR C 70 PHE 0.010 0.002 PHE C 83 TRP 0.003 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.20 ( 7940) covalent geometry : angle 0.60714 / 0.35 (11566) hydrogen bonds : bond 0.07178 / 7.52 ( 324) hydrogen bonds : angle 3.09719 / 3.98 ( 728) metal coordination : bond 0.01847 / 1.14 ( 4) metal coordination : angle 1.71403 / 2.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.152 Fit side-chains REVERT: C 58 GLN cc_start: 0.7308 (mt0) cc_final: 0.6105 (tp-100) REVERT: C 247 LYS cc_start: 0.7750 (ttmt) cc_final: 0.7204 (ttpt) REVERT: C 461 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5289 (tm-30) REVERT: C 580 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7286 (pt0) REVERT: C 739 LYS cc_start: 0.5431 (mmmt) cc_final: 0.4646 (ptpt) outliers start: 13 outliers final: 9 residues processed: 47 average time/residue: 0.4762 time to fit residues: 23.7625 Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.193118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148279 restraints weight = 6835.068| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 0.95 r_work: 0.3723 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7944 Z= 0.157 Angle : 0.561 10.202 11569 Z= 0.328 Chirality : 0.039 0.331 1430 Planarity : 0.005 0.058 793 Dihedral : 23.728 172.628 3191 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.74 % Allowed : 18.63 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.40), residues: 420 helix: 1.15 (0.39), residues: 177 sheet: -0.14 (1.35), residues: 10 loop : -0.75 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 556 TYR 0.011 0.002 TYR C 169 PHE 0.007 0.001 PHE C 83 TRP 0.003 0.001 TRP C 452 HIS 0.002 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 ( 7940) covalent geometry : angle 0.56078 / 0.33 (11566) hydrogen bonds : bond 0.05887 / 6.15 ( 324) hydrogen bonds : angle 3.02029 / 3.90 ( 728) metal coordination : bond 0.01076 / 0.68 ( 4) metal coordination : angle 1.42449 / 2.38 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.158 Fit side-chains REVERT: C 46 ASP cc_start: 0.7137 (m-30) cc_final: 0.6893 (m-30) REVERT: C 58 GLN cc_start: 0.7282 (mt0) cc_final: 0.6087 (tp-100) REVERT: C 247 LYS cc_start: 0.7735 (ttmt) cc_final: 0.7201 (ttpt) REVERT: C 461 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5260 (tm-30) REVERT: C 580 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: C 739 LYS cc_start: 0.5428 (mmmt) cc_final: 0.4684 (ptpt) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.4638 time to fit residues: 23.2042 Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.193033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148113 restraints weight = 6856.214| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.94 r_work: 0.3720 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7944 Z= 0.161 Angle : 0.563 6.658 11569 Z= 0.329 Chirality : 0.039 0.333 1430 Planarity : 0.005 0.057 793 Dihedral : 23.689 172.269 3191 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.74 % Allowed : 18.90 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.40), residues: 420 helix: 1.21 (0.38), residues: 177 sheet: -0.21 (1.33), residues: 10 loop : -0.78 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 556 TYR 0.011 0.002 TYR C 169 PHE 0.008 0.001 PHE C 83 TRP 0.004 0.001 TRP C 452 HIS 0.002 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 ( 7940) covalent geometry : angle 0.56211 / 0.33 (11566) hydrogen bonds : bond 0.05933 / 6.27 ( 324) hydrogen bonds : angle 3.01362 / 3.91 ( 728) metal coordination : bond 0.01456 / 0.93 ( 4) metal coordination : angle 1.43877 / 2.47 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.30 seconds wall clock time: 41 minutes 36.60 seconds (2496.60 seconds total)