Starting phenix.real_space_refine on Thu Jul 2 05:05:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8p_61237/07_2026/9j8p_61237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8p_61237/07_2026/9j8p_61237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j8p_61237/07_2026/9j8p_61237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8p_61237/07_2026/9j8p_61237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j8p_61237/07_2026/9j8p_61237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8p_61237/07_2026/9j8p_61237.map" } resolution = 3.21 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= 0.107 sd= 0.703 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 105 5.49 5 S 23 5.16 5 C 4029 2.51 5 N 1300 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 7061 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4804 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 37, 'TRANS': 585} Chain breaks: 3 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 2256 Classifications: {'RNA': 106} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 9, 'rna3p_pur': 46, 'rna3p_pyr': 40} Link IDs: {'rna2p': 20, 'rna3p': 85} Chain: "A" 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 98 SG CYS A 18 61.886 67.211 46.496 1.00 88.59 S ATOM 118 SG CYS A 21 64.743 64.526 46.908 1.00 89.17 S Time building chain proxies: 1.65, per 1000 atoms: 0.23 Number of scatterers: 7061 At special positions: 0 Unit cell: (102.09, 109.56, 124.5, 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 23 16.00 P 105 15.00 O 1603 8.00 N 1300 7.00 C 4029 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: 0.45 Conformation dependent library (CDL) restraints added in 264.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 34 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 40 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 21 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 18 " Number of angles added : 1 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 49.8% alpha, 12.2% beta 28 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 37 through 56 Processing helix chain 'A' and resid 68 through 80 removed outlier: 3.831A pdb=" N LEU A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 removed outlier: 3.647A pdb=" N GLN A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'A' and resid 173 through 195 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.611A pdb=" N VAL A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 403 removed outlier: 4.195A pdb=" N LEU A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 403 " --> pdb=" O CYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.691A pdb=" N ARG A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 505 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 556 through 575 removed outlier: 3.659A pdb=" N ARG A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.534A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 777 through 793 Processing helix chain 'A' and resid 799 through 817 removed outlier: 3.557A pdb=" N TRP A 803 " --> pdb=" O THR A 799 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 804 " --> pdb=" O ARG A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 873 Proline residue: A 867 - end of helix removed outlier: 3.713A pdb=" N ARG A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 removed outlier: 3.595A pdb=" N VAL A 23 " --> pdb=" O CYS A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 4.256A pdb=" N ASP A 218 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 217 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N SER A 383 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 219 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS A 372 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG A 357 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AA5, first strand: chain 'A' and resid 518 through 521 removed outlier: 6.813A pdb=" N SER A 510 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLN A 542 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU A 512 " --> pdb=" O GLN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 634 through 637 removed outlier: 3.545A pdb=" N ALA A 764 " --> pdb=" O VAL A 836 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER A 831 " --> pdb=" O LEU A 848 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1570 1.33 - 1.45: 2183 1.45 - 1.58: 3438 1.58 - 1.70: 210 1.70 - 1.82: 29 Bond restraints: 7430 Sorted by residual: bond pdb=" CE1 HIS A 772 " pdb=" NE2 HIS A 772 " ideal model delta sigma weight residual 1.321 1.352 -0.031 1.00e-02 1.00e+04 9.54e+00 bond pdb=" N TRP A 505 " pdb=" CA TRP A 505 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.25e-02 6.40e+03 7.66e+00 bond pdb=" ND1 HIS A 859 " pdb=" CE1 HIS A 859 " ideal model delta sigma weight residual 1.321 1.348 -0.027 1.00e-02 1.00e+04 7.28e+00 bond pdb=" N CYS A 504 " pdb=" CA CYS A 504 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.30e-02 5.92e+03 6.27e+00 bond pdb=" CZ ARG A 778 " pdb=" NH2 ARG A 778 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.15e+00 ... (remaining 7425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 9909 1.85 - 3.71: 567 3.71 - 5.56: 93 5.56 - 7.41: 10 7.41 - 9.27: 1 Bond angle restraints: 10580 Sorted by residual: angle pdb=" N ARG A 38 " pdb=" CA ARG A 38 " pdb=" C ARG A 38 " ideal model delta sigma weight residual 111.37 120.64 -9.27 1.64e+00 3.72e-01 3.19e+01 angle pdb=" CB HIS A 772 " pdb=" CG HIS A 772 " pdb=" CD2 HIS A 772 " ideal model delta sigma weight residual 131.20 124.36 6.84 1.30e+00 5.92e-01 2.77e+01 angle pdb=" OE1 GLN A 868 " pdb=" CD GLN A 868 " pdb=" NE2 GLN A 868 " ideal model delta sigma weight residual 122.60 117.69 4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" CB HIS A 634 " pdb=" CG HIS A 634 " pdb=" CD2 HIS A 634 " ideal model delta sigma weight residual 131.20 125.06 6.14 1.30e+00 5.92e-01 2.23e+01 angle pdb=" CB HIS A 859 " pdb=" CG HIS A 859 " pdb=" CD2 HIS A 859 " ideal model delta sigma weight residual 131.20 125.17 6.03 1.30e+00 5.92e-01 2.15e+01 ... (remaining 10575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.60: 4232 34.60 - 69.20: 288 69.20 - 103.79: 44 103.79 - 138.39: 5 138.39 - 172.99: 4 Dihedral angle restraints: 4573 sinusoidal: 2805 harmonic: 1768 Sorted by residual: dihedral pdb=" O4' U B 85 " pdb=" C1' U B 85 " pdb=" N1 U B 85 " pdb=" C2 U B 85 " ideal model delta sinusoidal sigma weight residual -160.00 -54.56 -105.44 1 1.50e+01 4.44e-03 5.40e+01 dihedral pdb=" CA CYS A 633 " pdb=" C CYS A 633 " pdb=" N HIS A 634 " pdb=" CA HIS A 634 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" O4' A B 82 " pdb=" C1' A B 82 " pdb=" N9 A B 82 " pdb=" C4 A B 82 " ideal model delta sinusoidal sigma weight residual 254.00 177.02 76.98 1 1.70e+01 3.46e-03 2.57e+01 ... (remaining 4570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 994 0.048 - 0.097: 187 0.097 - 0.145: 57 0.145 - 0.194: 23 0.194 - 0.242: 7 Chirality restraints: 1268 Sorted by residual: chirality pdb=" C3' G B 44 " pdb=" C4' G B 44 " pdb=" O3' G B 44 " pdb=" C2' G B 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA HIS A 379 " pdb=" N HIS A 379 " pdb=" C HIS A 379 " pdb=" CB HIS A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C1' A B 39 " pdb=" O4' A B 39 " pdb=" C2' A B 39 " pdb=" N9 A B 39 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1265 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 803 " -0.060 2.00e-02 2.50e+03 3.10e-02 2.40e+01 pdb=" CG TRP A 803 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP A 803 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 803 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A 803 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP A 803 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 803 " 0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 803 " -0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 803 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 803 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 855 " -0.050 2.00e-02 2.50e+03 3.11e-02 1.69e+01 pdb=" CG PHE A 855 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 855 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 855 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 855 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 855 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 855 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 36 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C GLY A 36 " 0.070 2.00e-02 2.50e+03 pdb=" O GLY A 36 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY A 37 " -0.024 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1165 2.77 - 3.30: 6782 3.30 - 3.83: 12700 3.83 - 4.37: 14501 4.37 - 4.90: 22078 Nonbonded interactions: 57226 Sorted by model distance: nonbonded pdb=" NH1 ARG A 558 " pdb=" OP1 G B 33 " model vdw 2.235 3.120 nonbonded pdb=" O ASP A 211 " pdb=" OD1 ASP A 211 " model vdw 2.237 3.040 nonbonded pdb=" O GLY A 525 " pdb=" OG SER A 528 " model vdw 2.239 3.040 nonbonded pdb=" O ALA A 107 " pdb=" OG SER A 110 " model vdw 2.262 3.040 nonbonded pdb=" O GLY A 54 " pdb=" OG SER A 57 " model vdw 2.284 3.040 ... (remaining 57221 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: 0.140 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.480 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.007 0.223 7434 Z= 0.388 Angle : 0.900 9.265 10581 Z= 0.636 Chirality : 0.049 0.242 1268 Planarity : 0.007 0.071 983 Dihedral : 20.973 172.991 3431 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: -0.46 (0.34), residues: 615 helix: 1.18 (0.31), residues: 285 sheet: -1.22 (0.49), residues: 92 loop : -1.77 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 778 TYR 0.010 0.001 TYR A 356 PHE 0.050 0.005 PHE A 855 TRP 0.060 0.009 TRP A 803 HIS 0.013 0.002 HIS A 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.38 ( 7430) covalent geometry : angle 0.90036 / 0.64 (10580) hydrogen bonds : bond 0.13777 / 9.78 ( 324) hydrogen bonds : angle 5.62549 / 4.04 ( 862) metal coordination : bond 0.11127 / 5.56 ( 4) metal coordination : angle 1.31894 / 0.69 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 TRP cc_start: 0.7984 (m-10) cc_final: 0.7716 (m-10) REVERT: A 577 LEU cc_start: 0.8518 (mt) cc_final: 0.8288 (tp) REVERT: A 832 PHE cc_start: 0.8048 (p90) cc_final: 0.7649 (p90) REVERT: A 858 LEU cc_start: 0.9518 (tp) cc_final: 0.9251 (mm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1320 time to fit residues: 11.8069 Evaluate side-chains 51 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 GLN ** A 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.103728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068870 restraints weight = 31294.319| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 4.10 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7434 Z= 0.225 Angle : 0.638 11.419 10581 Z= 0.338 Chirality : 0.039 0.261 1268 Planarity : 0.005 0.038 983 Dihedral : 23.581 169.189 2293 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.32 % Allowed : 7.16 % Favored : 90.52 % 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: -0.04 (0.33), residues: 615 helix: 1.55 (0.30), residues: 287 sheet: -0.61 (0.55), residues: 81 loop : -1.78 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 65 TYR 0.011 0.002 TYR A 356 PHE 0.020 0.002 PHE A 627 TRP 0.017 0.002 TRP A 803 HIS 0.009 0.001 HIS A 860 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 ( 7430) covalent geometry : angle 0.63813 / 0.34 (10580) hydrogen bonds : bond 0.06157 / 3.94 ( 324) hydrogen bonds : angle 4.57584 / 3.36 ( 862) metal coordination : bond 0.01577 / 0.78 ( 4) metal coordination : angle 0.23734 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8587 (t80) cc_final: 0.8259 (t80) REVERT: A 471 TRP cc_start: 0.8175 (m-10) cc_final: 0.7823 (m-10) REVERT: A 577 LEU cc_start: 0.8729 (mt) cc_final: 0.8498 (tp) REVERT: A 832 PHE cc_start: 0.8579 (p90) cc_final: 0.8208 (p90) REVERT: A 863 GLN cc_start: 0.9592 (mt0) cc_final: 0.9379 (mm-40) outliers start: 12 outliers final: 5 residues processed: 66 average time/residue: 0.1384 time to fit residues: 11.2238 Evaluate side-chains 54 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 422 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.103938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071663 restraints weight = 31082.309| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.92 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7434 Z= 0.149 Angle : 0.565 7.990 10581 Z= 0.303 Chirality : 0.037 0.264 1268 Planarity : 0.004 0.037 983 Dihedral : 23.525 168.675 2293 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.35 % Allowed : 11.99 % Favored : 86.65 % 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 (0.33), residues: 615 helix: 1.65 (0.30), residues: 289 sheet: -0.50 (0.57), residues: 83 loop : -1.66 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.009 0.001 TYR A 356 PHE 0.011 0.001 PHE A 203 TRP 0.011 0.001 TRP A 803 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 7430) covalent geometry : angle 0.56552 / 0.30 (10580) hydrogen bonds : bond 0.05358 / 3.34 ( 324) hydrogen bonds : angle 4.32774 / 3.16 ( 862) metal coordination : bond 0.00986 / 0.49 ( 4) metal coordination : angle 0.29817 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8632 (t80) cc_final: 0.8168 (t80) REVERT: A 334 LYS cc_start: 0.8804 (tptt) cc_final: 0.8562 (tppt) REVERT: A 471 TRP cc_start: 0.8215 (m-10) cc_final: 0.7872 (m-10) REVERT: A 532 GLU cc_start: 0.8293 (tp30) cc_final: 0.7906 (tp30) REVERT: A 577 LEU cc_start: 0.8760 (mt) cc_final: 0.8494 (tp) REVERT: A 832 PHE cc_start: 0.8176 (p90) cc_final: 0.7915 (p90) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.1396 time to fit residues: 10.1413 Evaluate side-chains 53 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 861 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 30.0000 chunk 44 optimal weight: 0.0980 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.103796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071768 restraints weight = 31303.447| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.91 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7434 Z= 0.150 Angle : 0.565 8.018 10581 Z= 0.302 Chirality : 0.037 0.273 1268 Planarity : 0.004 0.035 983 Dihedral : 23.466 168.361 2293 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.93 % Allowed : 10.64 % Favored : 87.43 % 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: 0.21 (0.34), residues: 615 helix: 1.71 (0.31), residues: 290 sheet: -0.61 (0.54), residues: 88 loop : -1.58 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 582 TYR 0.012 0.002 TYR A 75 PHE 0.010 0.002 PHE A 203 TRP 0.010 0.001 TRP A 803 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 7430) covalent geometry : angle 0.56456 / 0.30 (10580) hydrogen bonds : bond 0.05183 / 3.22 ( 324) hydrogen bonds : angle 4.22896 / 3.11 ( 862) metal coordination : bond 0.01268 / 0.63 ( 4) metal coordination : angle 0.38553 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7733 (m-70) REVERT: A 334 LYS cc_start: 0.8748 (tptt) cc_final: 0.8527 (tppt) REVERT: A 471 TRP cc_start: 0.8226 (m-10) cc_final: 0.7884 (m-10) REVERT: A 532 GLU cc_start: 0.8212 (tp30) cc_final: 0.7876 (tp30) REVERT: A 577 LEU cc_start: 0.8707 (mt) cc_final: 0.8469 (tp) REVERT: A 625 GLN cc_start: 0.8664 (tm-30) cc_final: 0.7825 (tm-30) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.1323 time to fit residues: 9.4127 Evaluate side-chains 52 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 861 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 69 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.103094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.068352 restraints weight = 31317.169| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.00 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7434 Z= 0.174 Angle : 0.589 9.916 10581 Z= 0.319 Chirality : 0.038 0.279 1268 Planarity : 0.005 0.080 983 Dihedral : 23.461 168.246 2293 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.74 % Allowed : 11.22 % Favored : 87.04 % 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: 0.19 (0.34), residues: 615 helix: 1.65 (0.30), residues: 290 sheet: -0.69 (0.55), residues: 83 loop : -1.50 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 784 TYR 0.010 0.001 TYR A 356 PHE 0.011 0.002 PHE A 832 TRP 0.015 0.001 TRP A 803 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 7430) covalent geometry : angle 0.58875 / 0.32 (10580) hydrogen bonds : bond 0.05326 / 3.32 ( 324) hydrogen bonds : angle 4.30211 / 3.18 ( 862) metal coordination : bond 0.01476 / 0.74 ( 4) metal coordination : angle 0.92273 / 0.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 TRP cc_start: 0.8216 (m-10) cc_final: 0.7873 (m-10) REVERT: A 532 GLU cc_start: 0.8410 (tp30) cc_final: 0.8009 (tp30) REVERT: A 625 GLN cc_start: 0.9363 (tm-30) cc_final: 0.9113 (tm-30) outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 0.1258 time to fit residues: 8.7642 Evaluate side-chains 52 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 861 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 50 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 30.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.100363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.069115 restraints weight = 30340.438| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.52 r_work: 0.2939 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7434 Z= 0.181 Angle : 0.621 13.628 10581 Z= 0.323 Chirality : 0.038 0.282 1268 Planarity : 0.004 0.036 983 Dihedral : 23.461 168.104 2293 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.55 % Allowed : 11.80 % Favored : 86.65 % 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 (0.34), residues: 615 helix: 1.66 (0.30), residues: 290 sheet: -0.77 (0.54), residues: 83 loop : -1.44 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 120 TYR 0.010 0.002 TYR A 356 PHE 0.010 0.002 PHE A 855 TRP 0.006 0.001 TRP A 589 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 7430) covalent geometry : angle 0.62083 / 0.32 (10580) hydrogen bonds : bond 0.05431 / 3.39 ( 324) hydrogen bonds : angle 4.29243 / 3.16 ( 862) metal coordination : bond 0.01526 / 0.76 ( 4) metal coordination : angle 1.67983 / 0.88 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 TRP cc_start: 0.8458 (m-10) cc_final: 0.8093 (m-10) REVERT: A 532 GLU cc_start: 0.8865 (tp30) cc_final: 0.8263 (tp30) REVERT: A 577 LEU cc_start: 0.9042 (mm) cc_final: 0.8658 (tp) REVERT: A 625 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9069 (tm-30) REVERT: A 813 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8947 (mm-30) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.1304 time to fit residues: 8.6867 Evaluate side-chains 52 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.100316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069023 restraints weight = 30328.901| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.50 r_work: 0.2937 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7434 Z= 0.168 Angle : 0.613 13.912 10581 Z= 0.319 Chirality : 0.038 0.279 1268 Planarity : 0.004 0.034 983 Dihedral : 23.461 167.821 2293 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.93 % Allowed : 11.61 % Favored : 86.46 % 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: 0.28 (0.34), residues: 615 helix: 1.73 (0.31), residues: 290 sheet: -0.75 (0.52), residues: 88 loop : -1.41 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 120 TYR 0.011 0.001 TYR A 356 PHE 0.010 0.002 PHE A 203 TRP 0.005 0.001 TRP A 416 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 7430) covalent geometry : angle 0.61244 / 0.32 (10580) hydrogen bonds : bond 0.05374 / 3.33 ( 324) hydrogen bonds : angle 4.26046 / 3.14 ( 862) metal coordination : bond 0.01361 / 0.68 ( 4) metal coordination : angle 1.88996 / 0.99 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8378 (tpm170) REVERT: A 471 TRP cc_start: 0.8441 (m-10) cc_final: 0.8081 (m-10) REVERT: A 532 GLU cc_start: 0.8824 (tp30) cc_final: 0.8337 (tp30) REVERT: A 577 LEU cc_start: 0.9057 (mm) cc_final: 0.8665 (tp) REVERT: A 582 ARG cc_start: 0.8305 (ttp80) cc_final: 0.7690 (ttp80) REVERT: A 625 GLN cc_start: 0.9370 (tm-30) cc_final: 0.9120 (tm-30) outliers start: 10 outliers final: 5 residues processed: 56 average time/residue: 0.1332 time to fit residues: 9.1072 Evaluate side-chains 53 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 58 optimal weight: 30.0000 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.100431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069000 restraints weight = 30752.385| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.56 r_work: 0.2938 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7434 Z= 0.158 Angle : 0.607 13.733 10581 Z= 0.314 Chirality : 0.038 0.278 1268 Planarity : 0.004 0.037 983 Dihedral : 23.442 167.541 2293 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.55 % Allowed : 11.61 % Favored : 86.85 % 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: 0.37 (0.34), residues: 615 helix: 1.77 (0.31), residues: 289 sheet: -0.72 (0.52), residues: 88 loop : -1.30 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 582 TYR 0.011 0.001 TYR A 356 PHE 0.011 0.002 PHE A 832 TRP 0.006 0.001 TRP A 531 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 7430) covalent geometry : angle 0.60667 / 0.31 (10580) hydrogen bonds : bond 0.05338 / 3.30 ( 324) hydrogen bonds : angle 4.21592 / 3.10 ( 862) metal coordination : bond 0.01147 / 0.57 ( 4) metal coordination : angle 1.81270 / 0.95 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8423 (tpm170) REVERT: A 90 ASP cc_start: 0.8612 (p0) cc_final: 0.8364 (p0) REVERT: A 116 LEU cc_start: 0.9118 (tp) cc_final: 0.8872 (tt) REVERT: A 471 TRP cc_start: 0.8441 (m-10) cc_final: 0.8018 (m-10) REVERT: A 505 TRP cc_start: 0.9321 (OUTLIER) cc_final: 0.8967 (m-10) REVERT: A 532 GLU cc_start: 0.8833 (tp30) cc_final: 0.8339 (tp30) REVERT: A 577 LEU cc_start: 0.9069 (mm) cc_final: 0.8657 (tp) REVERT: A 582 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7733 (ttp80) REVERT: A 625 GLN cc_start: 0.9362 (tm-30) cc_final: 0.9079 (tm-30) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.1462 time to fit residues: 9.7772 Evaluate side-chains 56 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 505 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.100410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069049 restraints weight = 30368.063| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.54 r_work: 0.2939 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7434 Z= 0.154 Angle : 0.618 12.891 10581 Z= 0.319 Chirality : 0.038 0.276 1268 Planarity : 0.004 0.039 983 Dihedral : 23.432 167.353 2293 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.16 % Allowed : 12.96 % Favored : 85.88 % 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: 0.28 (0.34), residues: 615 helix: 1.68 (0.31), residues: 290 sheet: -0.71 (0.52), residues: 88 loop : -1.37 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 628 TYR 0.010 0.001 TYR A 356 PHE 0.010 0.001 PHE A 832 TRP 0.007 0.001 TRP A 531 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 7430) covalent geometry : angle 0.61765 / 0.32 (10580) hydrogen bonds : bond 0.05287 / 3.26 ( 324) hydrogen bonds : angle 4.23722 / 3.14 ( 862) metal coordination : bond 0.01104 / 0.55 ( 4) metal coordination : angle 1.92852 / 1.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8773 (tpm170) cc_final: 0.7921 (tpm170) REVERT: A 471 TRP cc_start: 0.8455 (m-10) cc_final: 0.8066 (m-10) REVERT: A 505 TRP cc_start: 0.9314 (OUTLIER) cc_final: 0.9002 (m-10) REVERT: A 532 GLU cc_start: 0.8812 (tp30) cc_final: 0.8333 (tp30) REVERT: A 577 LEU cc_start: 0.9095 (mm) cc_final: 0.8678 (tp) REVERT: A 582 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7743 (ttp80) REVERT: A 625 GLN cc_start: 0.9412 (tm-30) cc_final: 0.9175 (tm-30) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.1409 time to fit residues: 9.4048 Evaluate side-chains 56 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 505 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.099792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.068396 restraints weight = 30486.162| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.55 r_work: 0.2920 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7434 Z= 0.189 Angle : 0.658 12.117 10581 Z= 0.345 Chirality : 0.039 0.285 1268 Planarity : 0.004 0.041 983 Dihedral : 23.439 167.391 2293 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.55 % Allowed : 12.38 % Favored : 86.07 % 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: 0.22 (0.34), residues: 615 helix: 1.59 (0.31), residues: 288 sheet: -0.70 (0.53), residues: 88 loop : -1.33 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 628 TYR 0.012 0.002 TYR A 356 PHE 0.010 0.002 PHE A 203 TRP 0.006 0.001 TRP A 416 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 7430) covalent geometry : angle 0.65721 / 0.34 (10580) hydrogen bonds : bond 0.05611 / 3.47 ( 324) hydrogen bonds : angle 4.35674 / 3.22 ( 862) metal coordination : bond 0.01371 / 0.68 ( 4) metal coordination : angle 2.49050 / 1.31 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 TRP cc_start: 0.9331 (OUTLIER) cc_final: 0.9020 (m-10) REVERT: A 532 GLU cc_start: 0.8810 (tp30) cc_final: 0.8318 (tp30) REVERT: A 577 LEU cc_start: 0.9075 (mm) cc_final: 0.8683 (tp) REVERT: A 582 ARG cc_start: 0.8360 (ttp80) cc_final: 0.7778 (ttp80) REVERT: A 625 GLN cc_start: 0.9425 (tm-30) cc_final: 0.9195 (tm-30) REVERT: A 814 LEU cc_start: 0.9104 (mt) cc_final: 0.8881 (mt) outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.1316 time to fit residues: 8.8034 Evaluate side-chains 58 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 505 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 70 optimal weight: 40.0000 chunk 38 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.100491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.069343 restraints weight = 29788.470| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.50 r_work: 0.2954 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7434 Z= 0.133 Angle : 0.613 12.358 10581 Z= 0.322 Chirality : 0.038 0.269 1268 Planarity : 0.005 0.091 983 Dihedral : 23.428 166.864 2293 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.16 % Allowed : 12.77 % Favored : 86.07 % 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: 0.32 (0.35), residues: 615 helix: 1.74 (0.31), residues: 288 sheet: -0.65 (0.54), residues: 88 loop : -1.38 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 558 TYR 0.008 0.001 TYR A 356 PHE 0.011 0.001 PHE A 832 TRP 0.009 0.001 TRP A 531 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7430) covalent geometry : angle 0.61309 / 0.32 (10580) hydrogen bonds : bond 0.05173 / 3.16 ( 324) hydrogen bonds : angle 4.29196 / 3.17 ( 862) metal coordination : bond 0.00791 / 0.39 ( 4) metal coordination : angle 1.82489 / 0.96 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.70 seconds wall clock time: 31 minutes 51.22 seconds (1911.22 seconds total)