Starting phenix.real_space_refine on Tue Aug 4 21:11:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8p_61237/08_2026/9j8p_61237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8p_61237/08_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_61237/08_2026/9j8p_61237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8p_61237/08_2026/9j8p_61237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j8p_61237/08_2026/9j8p_61237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8p_61237/08_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-2.2rc3-6140/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: 1.58, per 1000 atoms: 0.22 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: 0.63 Conformation dependent library (CDL) restraints added in 383.5 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: 1.00 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: 1.26 Time building geometry restraints manager: 0.86 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=" O3' A B 43 " pdb=" P G B 44 " ideal model delta sigma weight residual 1.607 1.640 -0.033 1.20e-02 6.94e+03 7.37e+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 ... (remaining 7425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 9692 1.85 - 3.71: 784 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: 904 0.048 - 0.097: 207 0.097 - 0.145: 131 0.145 - 0.194: 19 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=" 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 2.47 2.23 0.24 2.00e-01 2.50e+01 1.46e+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 ... (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: 0.120 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.120 Find NCS groups from input model: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.650 ------------------------------------------------------------------------------- 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= 0.398 Angle : 0.970 9.265 10581 Z= 0.701 Chirality : 0.059 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 0.00614 / 0.39 ( 7430) covalent geometry : angle 0.96959 / 0.70 (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 : 0.203 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: 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: 0.1528 time to fit residues: 13.6419 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 : 0.212 ------------------------------------------------------------------------------- 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: 20.0000 chunk 62 optimal weight: 40.0000 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 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4063 r_free = 0.4063 target = 0.103575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.068730 restraints weight = 31262.768| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.04 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7434 Z= 0.227 Angle : 0.660 11.620 10581 Z= 0.344 Chirality : 0.041 0.337 1268 Planarity : 0.005 0.034 983 Dihedral : 23.489 170.492 2293 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.51 % Allowed : 7.54 % Favored : 89.94 % 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: -0.06 (0.33), residues: 615 helix: 1.51 (0.30), residues: 287 sheet: -0.58 (0.55), residues: 81 loop : -1.76 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 581 TYR 0.011 0.002 TYR A 356 PHE 0.020 0.002 PHE A 627 TRP 0.016 0.002 TRP A 803 HIS 0.009 0.001 HIS A 860 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 ( 7430) covalent geometry : angle 0.65950 / 0.34 (10580) hydrogen bonds : bond 0.06235 / 3.95 ( 324) hydrogen bonds : angle 4.57368 / 3.35 ( 862) metal coordination : bond 0.01393 / 0.69 ( 4) metal coordination : angle 0.88000 / 0.46 ( 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 72 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.199 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: 0.8178 (m-10) cc_final: 0.7818 (m-10) REVERT: A 558 ARG cc_start: 0.7825 (ptt-90) cc_final: 0.7391 (ptt180) REVERT: A 577 LEU cc_start: 0.8722 (mt) cc_final: 0.8507 (tp) REVERT: A 832 PHE cc_start: 0.8595 (p90) cc_final: 0.8213 (p90) outliers start: 13 outliers final: 6 residues processed: 67 average time/residue: 0.1338 time to fit residues: 11.0439 Evaluate side-chains 55 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE 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: 0.9990 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.104803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072961 restraints weight = 31146.592| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.92 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7434 Z= 0.115 Angle : 0.569 11.689 10581 Z= 0.301 Chirality : 0.037 0.338 1268 Planarity : 0.004 0.032 983 Dihedral : 23.412 169.868 2293 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.35 % Allowed : 11.22 % 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: 0.17 (0.34), residues: 615 helix: 1.72 (0.31), residues: 289 sheet: -0.50 (0.57), residues: 83 loop : -1.70 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 585 TYR 0.008 0.001 TYR A 573 PHE 0.017 0.002 PHE A 59 TRP 0.011 0.001 TRP A 803 HIS 0.004 0.001 HIS A 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 7430) covalent geometry : angle 0.56878 / 0.30 (10580) hydrogen bonds : bond 0.05205 / 3.27 ( 324) hydrogen bonds : angle 4.29880 / 3.14 ( 862) metal coordination : bond 0.00279 / 0.14 ( 4) metal coordination : angle 0.14392 / 0.08 ( 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 : 0.208 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 22 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7968 (t-90) REVERT: A 116 LEU cc_start: 0.8764 (tt) cc_final: 0.8495 (tp) REVERT: A 471 TRP cc_start: 0.8153 (m-10) cc_final: 0.7893 (m-10) REVERT: A 532 GLU cc_start: 0.8325 (tp30) cc_final: 0.7937 (tp30) REVERT: A 558 ARG cc_start: 0.7700 (ptt-90) cc_final: 0.7219 (ptt180) REVERT: A 577 LEU cc_start: 0.8673 (mt) cc_final: 0.8429 (tp) REVERT: A 832 PHE cc_start: 0.8085 (p90) cc_final: 0.7820 (p90) outliers start: 7 outliers final: 1 residues processed: 60 average time/residue: 0.1415 time to fit residues: 10.4300 Evaluate side-chains 51 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 40.0000 chunk 44 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.102648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070251 restraints weight = 31204.070| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.94 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7434 Z= 0.213 Angle : 0.637 16.081 10581 Z= 0.330 Chirality : 0.040 0.354 1268 Planarity : 0.004 0.035 983 Dihedral : 23.403 170.280 2293 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.83 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: 0.12 (0.33), residues: 615 helix: 1.52 (0.30), residues: 289 sheet: -0.47 (0.56), residues: 83 loop : -1.51 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 783 TYR 0.011 0.002 TYR A 356 PHE 0.012 0.002 PHE A 203 TRP 0.011 0.002 TRP A 803 HIS 0.004 0.001 HIS A 860 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 ( 7430) covalent geometry : angle 0.63725 / 0.33 (10580) hydrogen bonds : bond 0.05932 / 3.67 ( 324) hydrogen bonds : angle 4.41867 / 3.24 ( 862) metal coordination : bond 0.02056 / 1.03 ( 4) metal coordination : angle 0.94019 / 0.49 ( 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 : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.8091 (t-90) REVERT: A 471 TRP cc_start: 0.8225 (m-10) cc_final: 0.7817 (m-10) REVERT: A 577 LEU cc_start: 0.8738 (mt) cc_final: 0.8504 (tp) REVERT: A 625 GLN cc_start: 0.8617 (tm-30) cc_final: 0.7762 (tm-30) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 0.1415 time to fit residues: 10.3535 Evaluate side-chains 53 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 69 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 overall best weight: 2.1502 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.101383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070170 restraints weight = 30321.120| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.55 r_work: 0.2964 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7434 Z= 0.140 Angle : 0.598 17.469 10581 Z= 0.310 Chirality : 0.039 0.343 1268 Planarity : 0.004 0.035 983 Dihedral : 23.399 169.706 2293 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.74 % Allowed : 11.99 % Favored : 86.27 % 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: 0.18 (0.34), residues: 615 helix: 1.62 (0.30), residues: 290 sheet: -0.69 (0.56), residues: 83 loop : -1.47 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 628 TYR 0.009 0.001 TYR A 356 PHE 0.014 0.002 PHE A 832 TRP 0.012 0.001 TRP A 803 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 7430) covalent geometry : angle 0.59828 / 0.31 (10580) hydrogen bonds : bond 0.05362 / 3.27 ( 324) hydrogen bonds : angle 4.24856 / 3.13 ( 862) metal coordination : bond 0.00928 / 0.46 ( 4) metal coordination : angle 0.85239 / 0.45 ( 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 61 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8574 (t70) REVERT: A 65 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8447 (tpm170) REVERT: A 91 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8499 (ptpp) REVERT: A 116 LEU cc_start: 0.9045 (tp) cc_final: 0.8821 (tt) REVERT: A 471 TRP cc_start: 0.8448 (m-10) cc_final: 0.8073 (m-10) REVERT: A 532 GLU cc_start: 0.8872 (tp30) cc_final: 0.8278 (tp30) REVERT: A 558 ARG cc_start: 0.8711 (ptt-90) cc_final: 0.8429 (ptt180) REVERT: A 577 LEU cc_start: 0.9053 (mt) cc_final: 0.8678 (tp) REVERT: A 582 ARG cc_start: 0.8403 (ttp80) cc_final: 0.7779 (ttp80) REVERT: A 625 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8915 (tm-30) REVERT: A 813 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8968 (mm-30) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 0.1421 time to fit residues: 10.1570 Evaluate side-chains 53 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 91 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 50 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 62 optimal weight: 40.0000 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 0.0670 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 30.0000 overall best weight: 3.1524 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.102442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069823 restraints weight = 31631.203| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.01 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7434 Z= 0.173 Angle : 0.607 16.558 10581 Z= 0.314 Chirality : 0.039 0.348 1268 Planarity : 0.005 0.054 983 Dihedral : 23.382 169.797 2293 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.74 % Allowed : 11.61 % 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: 0.19 (0.34), residues: 615 helix: 1.59 (0.30), residues: 290 sheet: -0.67 (0.56), residues: 83 loop : -1.41 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 783 TYR 0.011 0.001 TYR A 356 PHE 0.011 0.002 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 0.00380 / 0.17 ( 7430) covalent geometry : angle 0.60722 / 0.31 (10580) hydrogen bonds : bond 0.05613 / 3.41 ( 324) hydrogen bonds : angle 4.27836 / 3.14 ( 862) metal coordination : bond 0.01376 / 0.69 ( 4) metal coordination : angle 1.78760 / 0.94 ( 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 58 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8304 (tpm170) REVERT: A 91 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8460 (ptpp) REVERT: A 471 TRP cc_start: 0.8186 (m-10) cc_final: 0.7794 (m-10) REVERT: A 558 ARG cc_start: 0.7726 (ptt-90) cc_final: 0.7397 (ptt180) REVERT: A 625 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8588 (tm-30) REVERT: A 813 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8860 (mm-30) REVERT: A 859 HIS cc_start: 0.9202 (t-90) cc_final: 0.8939 (t-90) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.1381 time to fit residues: 9.4729 Evaluate side-chains 55 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG 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: 40.0000 chunk 42 optimal weight: 8.9990 chunk 58 optimal weight: 30.0000 chunk 61 optimal weight: 0.0060 chunk 40 optimal weight: 0.0370 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.102664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.071579 restraints weight = 30903.532| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.62 r_work: 0.3008 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7434 Z= 0.114 Angle : 0.604 18.734 10581 Z= 0.304 Chirality : 0.038 0.333 1268 Planarity : 0.004 0.034 983 Dihedral : 23.316 168.982 2293 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.97 % Allowed : 11.99 % 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: 0.41 (0.34), residues: 615 helix: 1.89 (0.31), residues: 290 sheet: -0.68 (0.55), residues: 83 loop : -1.41 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 120 TYR 0.007 0.001 TYR A 573 PHE 0.013 0.001 PHE A 832 TRP 0.013 0.001 TRP A 531 HIS 0.002 0.000 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7430) covalent geometry : angle 0.60379 / 0.30 (10580) hydrogen bonds : bond 0.04871 / 2.97 ( 324) hydrogen bonds : angle 4.03627 / 2.97 ( 862) metal coordination : bond 0.00201 / 0.10 ( 4) metal coordination : angle 0.90050 / 0.47 ( 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 56 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 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: 0.8745 (OUTLIER) cc_final: 0.8503 (tpm170) REVERT: A 471 TRP cc_start: 0.8391 (m-10) cc_final: 0.8002 (m-10) REVERT: A 532 GLU cc_start: 0.8940 (tp30) cc_final: 0.8383 (tp30) REVERT: A 577 LEU cc_start: 0.9075 (mm) cc_final: 0.8647 (tp) REVERT: A 625 GLN cc_start: 0.9302 (tm-30) cc_final: 0.9070 (tm-30) REVERT: A 813 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8976 (mm-30) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.1544 time to fit residues: 10.3231 Evaluate side-chains 54 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 787 GLN 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: 9.9990 chunk 58 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 63 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.100901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.069448 restraints weight = 30849.755| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.57 r_work: 0.2949 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7434 Z= 0.171 Angle : 0.647 18.061 10581 Z= 0.322 Chirality : 0.039 0.347 1268 Planarity : 0.004 0.036 983 Dihedral : 23.277 169.543 2293 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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: 0.45 (0.34), residues: 615 helix: 1.86 (0.30), residues: 290 sheet: -0.65 (0.56), residues: 83 loop : -1.31 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 120 TYR 0.011 0.001 TYR A 356 PHE 0.011 0.002 PHE A 203 TRP 0.010 0.001 TRP A 803 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 7430) covalent geometry : angle 0.64701 / 0.32 (10580) hydrogen bonds : bond 0.05408 / 3.30 ( 324) hydrogen bonds : angle 4.15372 / 3.06 ( 862) metal coordination : bond 0.01360 / 0.68 ( 4) metal coordination : angle 1.73898 / 0.92 ( 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 59 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.202 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: 0.8463 (m-10) cc_final: 0.8084 (m-10) REVERT: A 505 TRP cc_start: 0.9299 (OUTLIER) cc_final: 0.8989 (m-10) REVERT: A 532 GLU cc_start: 0.8776 (tp30) cc_final: 0.8301 (tp30) REVERT: A 577 LEU cc_start: 0.9068 (mm) cc_final: 0.8652 (tp) REVERT: A 625 GLN cc_start: 0.9322 (tm-30) cc_final: 0.9100 (tm-30) REVERT: A 813 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9011 (mm-30) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 0.1577 time to fit residues: 10.6671 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 : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 787 GLN 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: 9.9990 chunk 62 optimal weight: 50.0000 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.099628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068096 restraints weight = 30464.884| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.53 r_work: 0.2911 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7434 Z= 0.211 Angle : 0.685 18.636 10581 Z= 0.343 Chirality : 0.041 0.349 1268 Planarity : 0.004 0.039 983 Dihedral : 23.365 169.514 2293 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.74 % Allowed : 12.77 % Favored : 85.49 % 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: 0.29 (0.34), residues: 615 helix: 1.64 (0.31), residues: 289 sheet: -0.68 (0.53), residues: 88 loop : -1.27 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.013 0.002 TYR A 356 PHE 0.012 0.002 PHE A 203 TRP 0.015 0.001 TRP A 803 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 7430) covalent geometry : angle 0.68484 / 0.34 (10580) hydrogen bonds : bond 0.06001 / 3.67 ( 324) hydrogen bonds : angle 4.33901 / 3.18 ( 862) metal coordination : bond 0.02172 / 1.08 ( 4) metal coordination : angle 3.01966 / 1.59 ( 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 57 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8932 (p0) cc_final: 0.8418 (p0) REVERT: A 91 LYS cc_start: 0.8655 (ptpp) cc_final: 0.8380 (ptpp) REVERT: A 471 TRP cc_start: 0.8478 (m-10) cc_final: 0.8063 (m-10) REVERT: A 505 TRP cc_start: 0.9331 (OUTLIER) cc_final: 0.8962 (m-10) REVERT: A 577 LEU cc_start: 0.9073 (mm) cc_final: 0.8680 (tp) REVERT: A 625 GLN cc_start: 0.9301 (tm-30) cc_final: 0.9055 (tm-30) REVERT: A 813 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8878 (tm-30) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.1379 time to fit residues: 9.1821 Evaluate side-chains 55 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG 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 439 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 787 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.101095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.069698 restraints weight = 30611.220| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.57 r_work: 0.2956 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7434 Z= 0.131 Angle : 0.665 19.502 10581 Z= 0.331 Chirality : 0.039 0.336 1268 Planarity : 0.004 0.047 983 Dihedral : 23.331 168.788 2293 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.35 % Allowed : 13.54 % Favored : 85.11 % 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: 0.35 (0.34), residues: 615 helix: 1.68 (0.31), residues: 289 sheet: -0.50 (0.55), residues: 86 loop : -1.30 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 784 TYR 0.008 0.001 TYR A 356 PHE 0.012 0.001 PHE A 832 TRP 0.016 0.001 TRP A 803 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7430) covalent geometry : angle 0.66455 / 0.33 (10580) hydrogen bonds : bond 0.05272 / 3.19 ( 324) hydrogen bonds : angle 4.20584 / 3.09 ( 862) metal coordination : bond 0.00708 / 0.35 ( 4) metal coordination : angle 1.89081 / 1.00 ( 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 57 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8629 (mpp) REVERT: A 90 ASP cc_start: 0.8868 (p0) cc_final: 0.8336 (p0) REVERT: A 91 LYS cc_start: 0.8678 (ptpp) cc_final: 0.8419 (ptpp) REVERT: A 471 TRP cc_start: 0.8457 (m-10) cc_final: 0.8011 (m-10) REVERT: A 505 TRP cc_start: 0.9289 (OUTLIER) cc_final: 0.9000 (m-10) REVERT: A 532 GLU cc_start: 0.8794 (tp30) cc_final: 0.8325 (tp30) REVERT: A 577 LEU cc_start: 0.9081 (mm) cc_final: 0.8654 (tp) REVERT: A 582 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7593 (tmm-80) REVERT: A 625 GLN cc_start: 0.9347 (tm-30) cc_final: 0.9117 (tm-30) REVERT: A 813 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8973 (tm-30) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.1080 time to fit residues: 7.1643 Evaluate side-chains 55 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 87 MET 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 Chi-restraints excluded: chain A residue 787 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 66 optimal weight: 40.0000 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 70 optimal weight: 40.0000 chunk 38 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 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 = 0.4043 r_free = 0.4043 target = 0.101144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069824 restraints weight = 30307.433| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.55 r_work: 0.2960 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7434 Z= 0.135 Angle : 0.660 19.047 10581 Z= 0.331 Chirality : 0.039 0.338 1268 Planarity : 0.005 0.082 983 Dihedral : 23.285 168.853 2293 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.74 % Allowed : 13.54 % Favored : 84.72 % 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: 1.69 (0.31), residues: 287 sheet: -0.55 (0.56), residues: 88 loop : -1.32 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 558 TYR 0.009 0.001 TYR A 356 PHE 0.011 0.001 PHE A 832 TRP 0.014 0.001 TRP A 803 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 7430) covalent geometry : angle 0.65962 / 0.33 (10580) hydrogen bonds : bond 0.05311 / 3.22 ( 324) hydrogen bonds : angle 4.23179 / 3.10 ( 862) metal coordination : bond 0.00645 / 0.32 ( 4) metal coordination : angle 1.49936 / 0.79 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.70 seconds wall clock time: 33 minutes 18.90 seconds (1998.90 seconds total)