Starting phenix.real_space_refine on Thu Jul 2 06:31:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdr_60006/07_2026/8zdr_60006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdr_60006/07_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_60006/07_2026/8zdr_60006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdr_60006/07_2026/8zdr_60006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zdr_60006/07_2026/8zdr_60006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdr_60006/07_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-dev-6108/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: 1.69, per 1000 atoms: 0.23 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: 0.49 Conformation dependent library (CDL) restraints added in 234.8 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: 1.03 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: 1.30 Time building geometry restraints manager: 0.63 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: 11289 1.98 - 3.96: 254 3.96 - 5.94: 19 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 - 0.042: 1128 0.042 - 0.084: 209 0.084 - 0.126: 51 0.126 - 0.168: 26 0.168 - 0.210: 16 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 2.46 2.25 0.21 2.00e-01 2.50e+01 1.11e+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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.980 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:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- 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= 0.452 Angle : 0.708 9.899 11569 Z= 0.565 Chirality : 0.044 0.210 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 0.00561 / 0.45 ( 7940) covalent geometry : angle 0.70747 / 0.57 (11566) hydrogen bonds : bond 0.11473 / 10.29 ( 324) hydrogen bonds : angle 4.61892 / 6.34 ( 728) metal coordination : bond 0.00486 / 0.30 ( 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 : 0.173 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7285 (mt0) cc_final: 0.6471 (tp-100) REVERT: C 247 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7566 (ttpt) 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: 0.4412 time to fit residues: 20.2615 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 : 0.117 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 overall best weight: 1.3524 ------------------------------------------------------------------------------- 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 = 0.193167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148048 restraints weight = 6858.921| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 0.97 r_work: 0.3722 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7944 Z= 0.195 Angle : 0.603 7.275 11569 Z= 0.361 Chirality : 0.044 0.315 1430 Planarity : 0.005 0.059 793 Dihedral : 24.395 167.752 3191 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 13.97 % 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: -0.27 (0.39), residues: 420 helix: 0.46 (0.37), residues: 175 sheet: -0.14 (1.27), residues: 10 loop : -0.63 (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 0.005 0.001 TRP C 452 HIS 0.006 0.002 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.19 ( 7940) covalent geometry : angle 0.60269 / 0.36 (11566) hydrogen bonds : bond 0.07090 / 6.69 ( 324) hydrogen bonds : angle 3.36016 / 4.20 ( 728) metal coordination : bond 0.01329 / 0.85 ( 4) metal coordination : angle 1.64000 / 2.86 ( 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 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7270 (mt0) cc_final: 0.6149 (tp-100) REVERT: C 79 SER cc_start: 0.8321 (p) cc_final: 0.8075 (m) REVERT: C 239 HIS cc_start: 0.4408 (OUTLIER) cc_final: 0.4174 (m90) REVERT: C 247 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7200 (ttpt) REVERT: C 739 LYS cc_start: 0.5614 (mmmt) cc_final: 0.5122 (mtmm) outliers start: 9 outliers final: 3 residues processed: 44 average time/residue: 0.4363 time to fit residues: 20.5649 Evaluate side-chains 41 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.194910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150193 restraints weight = 6873.146| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 0.94 r_work: 0.3750 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7944 Z= 0.150 Angle : 0.534 8.325 11569 Z= 0.325 Chirality : 0.040 0.304 1430 Planarity : 0.004 0.041 793 Dihedral : 24.259 171.589 3191 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 14.79 % Favored : 82.74 % 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: 0.86 (0.38), residues: 177 sheet: -0.06 (1.34), residues: 10 loop : -0.62 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 63 TYR 0.011 0.001 TYR C 169 PHE 0.009 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 0.00259 / 0.15 ( 7940) covalent geometry : angle 0.53379 / 0.32 (11566) hydrogen bonds : bond 0.05701 / 5.29 ( 324) hydrogen bonds : angle 3.08395 / 3.82 ( 728) metal coordination : bond 0.00695 / 0.45 ( 4) metal coordination : angle 1.21735 / 2.03 ( 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 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 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: 0.6098 (tp-100) REVERT: C 79 SER cc_start: 0.8344 (p) cc_final: 0.8097 (m) REVERT: C 247 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7177 (ttpt) REVERT: C 621 LYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5669 (pttm) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 0.4296 time to fit residues: 21.6092 Evaluate side-chains 44 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 7.9990 chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.191983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146905 restraints weight = 6917.505| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 0.96 r_work: 0.3708 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7944 Z= 0.182 Angle : 0.570 8.151 11569 Z= 0.338 Chirality : 0.042 0.318 1430 Planarity : 0.005 0.037 793 Dihedral : 24.128 172.335 3191 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.84 % Allowed : 14.79 % Favored : 81.37 % 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: -0.03 (0.40), residues: 420 helix: 0.85 (0.38), residues: 177 sheet: -0.03 (1.32), residues: 10 loop : -0.68 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 137 TYR 0.012 0.002 TYR C 169 PHE 0.010 0.002 PHE C 648 TRP 0.002 0.001 TRP C 452 HIS 0.004 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 ( 7940) covalent geometry : angle 0.56953 / 0.34 (11566) hydrogen bonds : bond 0.06560 / 6.08 ( 324) hydrogen bonds : angle 3.06145 / 3.82 ( 728) metal coordination : bond 0.01349 / 0.87 ( 4) metal coordination : angle 1.42585 / 2.40 ( 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 54 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7301 (mt0) cc_final: 0.6157 (tp-100) REVERT: C 79 SER cc_start: 0.8401 (p) cc_final: 0.8169 (m) REVERT: C 247 LYS cc_start: 0.7748 (ttmt) cc_final: 0.7201 (ttpt) REVERT: C 696 LEU cc_start: 0.7463 (mp) cc_final: 0.7232 (tp) REVERT: C 739 LYS cc_start: 0.5460 (mmmt) cc_final: 0.4839 (ptpt) outliers start: 14 outliers final: 6 residues processed: 50 average time/residue: 0.4079 time to fit residues: 21.8982 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR 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: 0.8980 chunk 34 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.191656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146745 restraints weight = 6901.862| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 0.95 r_work: 0.3704 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7944 Z= 0.189 Angle : 0.570 8.067 11569 Z= 0.338 Chirality : 0.042 0.314 1430 Planarity : 0.005 0.041 793 Dihedral : 24.050 173.185 3191 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.47 % Allowed : 17.53 % 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: -0.11 (0.39), residues: 420 helix: 0.78 (0.38), residues: 177 sheet: 0.09 (1.36), residues: 10 loop : -0.74 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 672 TYR 0.012 0.002 TYR C 169 PHE 0.009 0.002 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 0.00345 / 0.19 ( 7940) covalent geometry : angle 0.56930 / 0.34 (11566) hydrogen bonds : bond 0.06648 / 6.14 ( 324) hydrogen bonds : angle 3.12378 / 3.94 ( 728) metal coordination : bond 0.01503 / 0.97 ( 4) metal coordination : angle 1.63460 / 2.73 ( 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 52 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7328 (mt0) cc_final: 0.6137 (tp-100) REVERT: C 79 SER cc_start: 0.8416 (p) cc_final: 0.8190 (m) REVERT: C 247 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7304 (ttpt) REVERT: C 580 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7122 (pt0) REVERT: C 696 LEU cc_start: 0.7483 (mp) cc_final: 0.7272 (tp) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.5014 time to fit residues: 25.5443 Evaluate side-chains 47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR 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 580 GLU Chi-restraints excluded: chain C residue 614 GLU 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: 2.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 0.0010 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.3592 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.188575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143451 restraints weight = 6869.773| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.08 r_work: 0.3666 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7944 Z= 0.257 Angle : 0.652 7.883 11569 Z= 0.373 Chirality : 0.047 0.323 1430 Planarity : 0.006 0.047 793 Dihedral : 24.056 172.953 3191 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.29 % Allowed : 18.08 % 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: -0.44 (0.38), residues: 420 helix: 0.43 (0.37), residues: 177 sheet: -0.01 (1.26), residues: 10 loop : -0.85 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 556 TYR 0.013 0.002 TYR C 70 PHE 0.012 0.002 PHE C 83 TRP 0.003 0.001 TRP C 452 HIS 0.004 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.26 ( 7940) covalent geometry : angle 0.65077 / 0.37 (11566) hydrogen bonds : bond 0.08423 / 7.85 ( 324) hydrogen bonds : angle 3.23970 / 4.03 ( 728) metal coordination : bond 0.02112 / 1.35 ( 4) metal coordination : angle 2.09088 / 3.51 ( 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 53 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.156 Fit side-chains REVERT: C 58 GLN cc_start: 0.7355 (mt0) cc_final: 0.6135 (tp-100) REVERT: C 79 SER cc_start: 0.8442 (p) cc_final: 0.8214 (m) REVERT: C 247 LYS cc_start: 0.7772 (ttmt) cc_final: 0.7226 (ttpt) REVERT: C 461 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5262 (tm-30) REVERT: C 577 CYS cc_start: 0.7378 (t) cc_final: 0.7156 (t) REVERT: C 580 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7263 (pt0) REVERT: C 696 LEU cc_start: 0.7538 (mp) cc_final: 0.7292 (tp) REVERT: C 739 LYS cc_start: 0.5543 (mmmt) cc_final: 0.4693 (ptpt) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.4936 time to fit residues: 26.2039 Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.193997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149594 restraints weight = 6902.809| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 0.94 r_work: 0.3744 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1735 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= 0.145 Angle : 0.532 8.710 11569 Z= 0.320 Chirality : 0.039 0.303 1430 Planarity : 0.004 0.033 793 Dihedral : 23.987 174.084 3191 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.47 % Allowed : 18.63 % 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: 0.05 (0.40), residues: 420 helix: 1.02 (0.38), residues: 177 sheet: 0.17 (1.45), residues: 10 loop : -0.74 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 556 TYR 0.011 0.001 TYR C 169 PHE 0.006 0.001 PHE C 648 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 0.00256 / 0.15 ( 7940) covalent geometry : angle 0.53163 / 0.32 (11566) hydrogen bonds : bond 0.05536 / 5.07 ( 324) hydrogen bonds : angle 3.01487 / 3.79 ( 728) metal coordination : bond 0.00782 / 0.51 ( 4) metal coordination : angle 1.27652 / 2.14 ( 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 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.210 Fit side-chains REVERT: C 58 GLN cc_start: 0.7282 (mt0) cc_final: 0.6102 (tp-100) REVERT: C 247 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7233 (ttpt) REVERT: C 461 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.5244 (tm-30) REVERT: C 580 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: C 739 LYS cc_start: 0.5433 (mmmt) cc_final: 0.4675 (ptpt) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.5264 time to fit residues: 26.9375 Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 10.0000 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.192782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147904 restraints weight = 6898.120| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 0.96 r_work: 0.3715 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7944 Z= 0.164 Angle : 0.542 7.794 11569 Z= 0.325 Chirality : 0.040 0.310 1430 Planarity : 0.004 0.035 793 Dihedral : 23.885 173.415 3191 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.01 % Allowed : 19.18 % Favored : 77.81 % 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: 0.13 (0.40), residues: 420 helix: 1.14 (0.39), residues: 177 sheet: -0.04 (1.39), residues: 10 loop : -0.73 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 556 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 0.00297 / 0.16 ( 7940) covalent geometry : angle 0.54132 / 0.33 (11566) hydrogen bonds : bond 0.05890 / 5.49 ( 324) hydrogen bonds : angle 2.99564 / 3.78 ( 728) metal coordination : bond 0.01170 / 0.76 ( 4) metal coordination : angle 1.40508 / 2.38 ( 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 54 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.178 Fit side-chains REVERT: C 46 ASP cc_start: 0.7089 (m-30) cc_final: 0.6841 (m-30) REVERT: C 58 GLN cc_start: 0.7299 (mt0) cc_final: 0.6128 (tp-100) REVERT: C 79 SER cc_start: 0.8386 (p) cc_final: 0.8184 (m) REVERT: C 215 GLU cc_start: 0.5435 (tp30) cc_final: 0.5222 (mt-10) REVERT: C 247 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7230 (ttpt) REVERT: C 263 PHE cc_start: 0.7460 (m-80) cc_final: 0.7185 (m-80) REVERT: C 461 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5216 (tm-30) REVERT: C 580 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7253 (pt0) outliers start: 11 outliers final: 6 residues processed: 51 average time/residue: 0.4405 time to fit residues: 24.0067 Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.192149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147323 restraints weight = 6789.073| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 0.94 r_work: 0.3708 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7944 Z= 0.178 Angle : 0.571 9.580 11569 Z= 0.336 Chirality : 0.041 0.309 1430 Planarity : 0.005 0.060 793 Dihedral : 23.833 173.338 3191 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.47 % Allowed : 20.00 % Favored : 77.53 % 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: -0.01 (0.40), residues: 420 helix: 1.00 (0.39), residues: 177 sheet: -0.10 (1.34), residues: 10 loop : -0.79 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 65 TYR 0.011 0.002 TYR C 169 PHE 0.008 0.001 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 0.00329 / 0.18 ( 7940) covalent geometry : angle 0.57036 / 0.34 (11566) hydrogen bonds : bond 0.06182 / 5.83 ( 324) hydrogen bonds : angle 3.10188 / 3.98 ( 728) metal coordination : bond 0.01280 / 0.83 ( 4) metal coordination : angle 1.47453 / 2.47 ( 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 52 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.180 Fit side-chains REVERT: C 46 ASP cc_start: 0.7187 (m-30) cc_final: 0.6933 (m-30) REVERT: C 58 GLN cc_start: 0.7319 (mt0) cc_final: 0.6126 (tp-100) REVERT: C 79 SER cc_start: 0.8399 (p) cc_final: 0.8195 (m) REVERT: C 215 GLU cc_start: 0.5262 (tp30) cc_final: 0.5024 (mt-10) REVERT: C 247 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7300 (ttpt) REVERT: C 263 PHE cc_start: 0.7440 (m-80) cc_final: 0.7163 (m-80) REVERT: C 461 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5236 (tm-30) REVERT: C 577 CYS cc_start: 0.7319 (t) cc_final: 0.7093 (t) REVERT: C 580 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7312 (pt0) REVERT: C 739 LYS cc_start: 0.5488 (mmmt) cc_final: 0.4494 (ptpt) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.4539 time to fit residues: 23.3230 Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 197 VAL 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: 1.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.193358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148700 restraints weight = 6840.196| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 0.94 r_work: 0.3727 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7944 Z= 0.152 Angle : 0.548 9.626 11569 Z= 0.327 Chirality : 0.039 0.306 1430 Planarity : 0.005 0.072 793 Dihedral : 23.848 173.183 3191 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.47 % Allowed : 20.27 % Favored : 77.26 % 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: 1.19 (0.39), residues: 177 sheet: -0.23 (1.33), residues: 10 loop : -0.76 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 65 TYR 0.011 0.001 TYR C 169 PHE 0.006 0.001 PHE C 596 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 0.00278 / 0.15 ( 7940) covalent geometry : angle 0.54805 / 0.33 (11566) hydrogen bonds : bond 0.05759 / 5.40 ( 324) hydrogen bonds : angle 3.06019 / 3.90 ( 728) metal coordination : bond 0.00851 / 0.56 ( 4) metal coordination : angle 1.41743 / 2.39 ( 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: 9 poor density : 42 time to evaluate : 0.175 Fit side-chains REVERT: C 46 ASP cc_start: 0.7061 (m-30) cc_final: 0.6807 (m-30) REVERT: C 58 GLN cc_start: 0.7296 (mt0) cc_final: 0.6111 (tp-100) REVERT: C 247 LYS cc_start: 0.7769 (ttmt) cc_final: 0.7278 (ttpt) REVERT: C 263 PHE cc_start: 0.7433 (m-80) cc_final: 0.7162 (m-80) REVERT: C 461 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5214 (tm-30) REVERT: C 577 CYS cc_start: 0.7353 (t) cc_final: 0.7115 (t) REVERT: C 580 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: C 739 LYS cc_start: 0.5263 (mmmt) cc_final: 0.4326 (ptpt) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.4072 time to fit residues: 21.3074 Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.0030 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 = 0.194800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150279 restraints weight = 6864.073| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 0.95 r_work: 0.3748 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7944 Z= 0.145 Angle : 0.529 9.039 11569 Z= 0.317 Chirality : 0.038 0.302 1430 Planarity : 0.004 0.051 793 Dihedral : 23.777 173.253 3191 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.92 % Allowed : 20.82 % Favored : 77.26 % 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: 0.16 (0.40), residues: 420 helix: 1.21 (0.38), residues: 182 sheet: -0.30 (1.32), residues: 10 loop : -0.79 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 556 TYR 0.010 0.001 TYR C 169 PHE 0.005 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 0.00260 / 0.15 ( 7940) covalent geometry : angle 0.52889 / 0.32 (11566) hydrogen bonds : bond 0.05148 / 4.89 ( 324) hydrogen bonds : angle 3.01593 / 3.86 ( 728) metal coordination : bond 0.00848 / 0.55 ( 4) metal coordination : angle 1.19819 / 2.02 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.42 seconds wall clock time: 40 minutes 0.27 seconds (2400.27 seconds total)