Starting phenix.real_space_refine on Wed Sep 17 07:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8p_61237/09_2025/9j8p_61237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8p_61237/09_2025/9j8p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j8p_61237/09_2025/9j8p_61237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8p_61237/09_2025/9j8p_61237.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8p_61237/09_2025/9j8p_61237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8p_61237/09_2025/9j8p_61237.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 1.61, 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: 0.54 Conformation dependent library (CDL) restraints added in 278.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.85 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: 1.38 Time building geometry restraints manager: 0.75 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: 0.120 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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= 0.375 Angle : 0.900 9.265 10581 Z= 0.584 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 aren 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 covalent geometry : bond 0.00607 ( 7430) covalent geometry : angle 0.90033 (10580) hydrogen bonds : bond 0.13777 ( 324) hydrogen bonds : angle 5.62549 ( 862) metal coordination : bond 0.11127 ( 4) metal coordination : angle 1.31894 ( 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 : 0.217 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: 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: 0.1657 time to fit residues: 14.6568 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 : 0.209 ------------------------------------------------------------------------------- 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: 20.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4043 r_free = 0.4043 target = 0.102507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.067545 restraints weight = 31270.271| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.99 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1881 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= 0.238 Angle : 0.682 10.331 10581 Z= 0.341 Chirality : 0.040 0.293 1268 Planarity : 0.005 0.038 983 Dihedral : 23.564 168.976 2293 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.13 % Allowed : 8.32 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.33), residues: 615 helix: 1.52 (0.30), residues: 288 sheet: -0.65 (0.57), residues: 76 loop : -1.64 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 445 TYR 0.012 0.002 TYR A 356 PHE 0.019 0.002 PHE A 627 TRP 0.012 0.002 TRP A 803 HIS 0.007 0.001 HIS A 860 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 7430) covalent geometry : angle 0.68227 (10580) hydrogen bonds : bond 0.05934 ( 324) hydrogen bonds : angle 4.45123 ( 862) metal coordination : bond 0.01471 ( 4) metal coordination : angle 0.26787 ( 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 69 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 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 471 TRP cc_start: 0.8223 (m-10) cc_final: 0.7822 (m-10) REVERT: A 804 LEU cc_start: 0.9765 (mt) cc_final: 0.9518 (mt) REVERT: A 813 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8835 (mm-30) REVERT: A 832 PHE cc_start: 0.8701 (p90) cc_final: 0.8356 (p90) REVERT: A 858 LEU cc_start: 0.9695 (tp) cc_final: 0.9362 (mm) REVERT: A 863 GLN cc_start: 0.9590 (mt0) cc_final: 0.9343 (mm-40) outliers start: 11 outliers final: 3 residues processed: 66 average time/residue: 0.1467 time to fit residues: 11.7865 Evaluate side-chains 50 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 422 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 23 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 565 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.103262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070715 restraints weight = 31088.131| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.07 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7434 Z= 0.144 Angle : 0.587 10.019 10581 Z= 0.293 Chirality : 0.037 0.273 1268 Planarity : 0.004 0.035 983 Dihedral : 23.410 167.638 2293 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.55 % Allowed : 10.25 % Favored : 88.20 % 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 aren not related in a simple way. whole: 0.40 (0.34), residues: 615 helix: 2.02 (0.30), residues: 289 sheet: -1.01 (0.52), residues: 93 loop : -1.47 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.010 0.001 TYR A 356 PHE 0.013 0.001 PHE A 627 TRP 0.009 0.001 TRP A 531 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7430) covalent geometry : angle 0.58699 (10580) hydrogen bonds : bond 0.04886 ( 324) hydrogen bonds : angle 4.09140 ( 862) metal coordination : bond 0.01162 ( 4) metal coordination : angle 0.82266 ( 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 63 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 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 22 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7883 (t-90) REVERT: A 59 PHE cc_start: 0.8625 (t80) cc_final: 0.8282 (t80) REVERT: A 116 LEU cc_start: 0.8809 (tt) cc_final: 0.8565 (tp) REVERT: A 471 TRP cc_start: 0.8187 (m-10) cc_final: 0.7843 (m-10) REVERT: A 505 TRP cc_start: 0.9235 (OUTLIER) cc_final: 0.8913 (m-10) REVERT: A 532 GLU cc_start: 0.8230 (tp30) cc_final: 0.7882 (tp30) REVERT: A 813 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8779 (mm-30) REVERT: A 858 LEU cc_start: 0.9605 (tp) cc_final: 0.9299 (mm) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.1462 time to fit residues: 10.8720 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 : 0.179 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 505 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 44 optimal weight: 0.0040 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4055 r_free = 0.4055 target = 0.101677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.071051 restraints weight = 30628.852| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.44 r_work: 0.2969 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7434 Z= 0.126 Angle : 0.581 11.725 10581 Z= 0.289 Chirality : 0.036 0.270 1268 Planarity : 0.004 0.033 983 Dihedral : 23.317 167.249 2293 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.35 % Allowed : 11.03 % Favored : 87.62 % 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 aren not related in a simple way. whole: 0.59 (0.34), residues: 615 helix: 2.16 (0.31), residues: 290 sheet: -0.59 (0.55), residues: 86 loop : -1.52 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 558 TYR 0.009 0.001 TYR A 356 PHE 0.011 0.001 PHE A 832 TRP 0.008 0.001 TRP A 531 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7430) covalent geometry : angle 0.58070 (10580) hydrogen bonds : bond 0.04693 ( 324) hydrogen bonds : angle 3.97909 ( 862) metal coordination : bond 0.00831 ( 4) metal coordination : angle 1.09844 ( 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 61 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8866 (OUTLIER) cc_final: 0.8401 (t-90) REVERT: A 59 PHE cc_start: 0.8878 (t80) cc_final: 0.8469 (t80) REVERT: A 90 ASP cc_start: 0.8703 (p0) cc_final: 0.8422 (p0) REVERT: A 116 LEU cc_start: 0.8920 (tt) cc_final: 0.8647 (tp) REVERT: A 471 TRP cc_start: 0.8455 (m-10) cc_final: 0.8059 (m-10) REVERT: A 532 GLU cc_start: 0.8898 (tp30) cc_final: 0.8360 (tp30) REVERT: A 577 LEU cc_start: 0.9090 (mm) cc_final: 0.8787 (tp) REVERT: A 813 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9083 (mm-30) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.1321 time to fit residues: 9.3531 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 : 0.170 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 381 ASP 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: 0.0000 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 565 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.101162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069686 restraints weight = 30496.936| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.55 r_work: 0.2964 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7434 Z= 0.137 Angle : 0.606 14.282 10581 Z= 0.295 Chirality : 0.037 0.269 1268 Planarity : 0.004 0.044 983 Dihedral : 23.287 167.120 2293 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.90 % Allowed : 10.25 % 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 aren not related in a simple way. whole: 0.56 (0.34), residues: 615 helix: 2.02 (0.31), residues: 290 sheet: -0.57 (0.54), residues: 86 loop : -1.38 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 558 TYR 0.009 0.001 TYR A 356 PHE 0.033 0.002 PHE A 627 TRP 0.008 0.001 TRP A 803 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7430) covalent geometry : angle 0.60549 (10580) hydrogen bonds : bond 0.04851 ( 324) hydrogen bonds : angle 4.04501 ( 862) metal coordination : bond 0.01027 ( 4) metal coordination : angle 1.52978 ( 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 65 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.8448 (t-90) REVERT: A 41 ARG cc_start: 0.8856 (mtm-85) cc_final: 0.8563 (mtm-85) REVERT: A 59 PHE cc_start: 0.8890 (t80) cc_final: 0.8421 (t80) REVERT: A 471 TRP cc_start: 0.8474 (m-10) cc_final: 0.8078 (m-10) REVERT: A 505 TRP cc_start: 0.9271 (OUTLIER) cc_final: 0.8993 (m-10) REVERT: A 532 GLU cc_start: 0.8807 (tp30) cc_final: 0.8312 (tp30) REVERT: A 577 LEU cc_start: 0.9116 (mm) cc_final: 0.8788 (tp) REVERT: A 784 ARG cc_start: 0.9659 (mmt-90) cc_final: 0.9424 (mmt-90) REVERT: A 787 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.6098 (mp10) REVERT: A 813 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9152 (tm-30) outliers start: 15 outliers final: 5 residues processed: 61 average time/residue: 0.1378 time to fit residues: 10.1219 Evaluate side-chains 56 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 803 TRP 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: 10.0000 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 188 GLN A 565 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.099972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067432 restraints weight = 31271.632| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.02 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7434 Z= 0.242 Angle : 0.699 13.044 10581 Z= 0.343 Chirality : 0.040 0.283 1268 Planarity : 0.005 0.041 983 Dihedral : 23.512 167.298 2293 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.32 % Allowed : 10.44 % Favored : 87.23 % 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 aren not related in a simple way. whole: 0.33 (0.34), residues: 615 helix: 1.63 (0.30), residues: 290 sheet: -0.59 (0.56), residues: 86 loop : -1.25 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 558 TYR 0.014 0.002 TYR A 356 PHE 0.012 0.002 PHE A 203 TRP 0.006 0.001 TRP A 589 HIS 0.004 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 7430) covalent geometry : angle 0.69904 (10580) hydrogen bonds : bond 0.06235 ( 324) hydrogen bonds : angle 4.38474 ( 862) metal coordination : bond 0.02276 ( 4) metal coordination : angle 2.42419 ( 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 65 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.8034 (t-90) REVERT: A 41 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.8383 (mtm-85) REVERT: A 65 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8242 (tpm170) REVERT: A 87 MET cc_start: 0.8373 (mmm) cc_final: 0.8147 (mmm) REVERT: A 505 TRP cc_start: 0.9242 (OUTLIER) cc_final: 0.8910 (m-10) REVERT: A 532 GLU cc_start: 0.8273 (tp30) cc_final: 0.8031 (tp30) REVERT: A 577 LEU cc_start: 0.8872 (mm) cc_final: 0.8598 (tp) REVERT: A 582 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7171 (ttp80) REVERT: A 787 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.6205 (mp10) REVERT: A 814 LEU cc_start: 0.9185 (mt) cc_final: 0.8856 (mt) outliers start: 12 outliers final: 7 residues processed: 63 average time/residue: 0.1404 time to fit residues: 10.6699 Evaluate side-chains 57 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 438 VAL 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 Chi-restraints excluded: chain A residue 803 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.099437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.068823 restraints weight = 30502.146| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.44 r_work: 0.2912 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3226 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= 0.156 Angle : 0.640 12.241 10581 Z= 0.317 Chirality : 0.038 0.267 1268 Planarity : 0.005 0.043 983 Dihedral : 23.395 166.259 2293 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.13 % Allowed : 12.19 % Favored : 85.69 % 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 aren not related in a simple way. whole: 0.45 (0.34), residues: 615 helix: 1.79 (0.30), residues: 292 sheet: -0.52 (0.56), residues: 86 loop : -1.30 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 558 TYR 0.010 0.002 TYR A 356 PHE 0.010 0.001 PHE A 203 TRP 0.006 0.001 TRP A 531 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7430) covalent geometry : angle 0.63943 (10580) hydrogen bonds : bond 0.05379 ( 324) hydrogen bonds : angle 4.23213 ( 862) metal coordination : bond 0.00963 ( 4) metal coordination : angle 1.95977 ( 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 62 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8373 (t-90) REVERT: A 41 ARG cc_start: 0.8889 (mtm-85) cc_final: 0.8679 (mtm-85) REVERT: A 65 ARG cc_start: 0.8614 (tpm170) cc_final: 0.8336 (tpm170) REVERT: A 505 TRP cc_start: 0.9302 (OUTLIER) cc_final: 0.9029 (m-10) REVERT: A 532 GLU cc_start: 0.8822 (tp30) cc_final: 0.8356 (tp30) REVERT: A 577 LEU cc_start: 0.9097 (mm) cc_final: 0.8784 (tp) REVERT: A 582 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7820 (ttp80) REVERT: A 625 GLN cc_start: 0.9459 (tm-30) cc_final: 0.9101 (pp30) REVERT: A 787 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6449 (mp10) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.1655 time to fit residues: 12.2479 Evaluate side-chains 54 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 803 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 30.0000 chunk 28 optimal weight: 0.6980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.100682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067885 restraints weight = 31084.916| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.04 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3445 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= 0.187 Angle : 0.680 12.381 10581 Z= 0.333 Chirality : 0.039 0.258 1268 Planarity : 0.005 0.042 983 Dihedral : 23.417 166.377 2293 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.13 % Allowed : 14.12 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.34), residues: 615 helix: 1.66 (0.30), residues: 292 sheet: -0.48 (0.57), residues: 86 loop : -1.28 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 558 TYR 0.012 0.002 TYR A 356 PHE 0.010 0.002 PHE A 203 TRP 0.005 0.001 TRP A 416 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7430) covalent geometry : angle 0.67923 (10580) hydrogen bonds : bond 0.05718 ( 324) hydrogen bonds : angle 4.28589 ( 862) metal coordination : bond 0.01258 ( 4) metal coordination : angle 2.62913 ( 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 60 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.8158 (t-90) REVERT: A 41 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8329 (mtm-85) REVERT: A 65 ARG cc_start: 0.8529 (tpm170) cc_final: 0.8239 (tpm170) REVERT: A 505 TRP cc_start: 0.9216 (OUTLIER) cc_final: 0.8951 (m-10) REVERT: A 532 GLU cc_start: 0.8260 (tp30) cc_final: 0.7979 (tp30) REVERT: A 577 LEU cc_start: 0.8896 (mm) cc_final: 0.8574 (tp) REVERT: A 582 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7331 (ttp80) REVERT: A 625 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8578 (pp30) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.1648 time to fit residues: 11.7490 Evaluate side-chains 53 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 439 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 803 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** 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 = 0.3991 r_free = 0.3991 target = 0.099160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.066612 restraints weight = 30810.320| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.33 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7434 Z= 0.254 Angle : 0.777 16.891 10581 Z= 0.374 Chirality : 0.041 0.256 1268 Planarity : 0.005 0.048 983 Dihedral : 23.552 166.202 2293 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.13 % Allowed : 14.70 % Favored : 83.17 % 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 aren not related in a simple way. whole: 0.07 (0.34), residues: 615 helix: 1.43 (0.30), residues: 288 sheet: -0.78 (0.54), residues: 88 loop : -1.34 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 120 TYR 0.012 0.002 TYR A 356 PHE 0.012 0.002 PHE A 203 TRP 0.007 0.001 TRP A 589 HIS 0.004 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 7430) covalent geometry : angle 0.77637 (10580) hydrogen bonds : bond 0.06193 ( 324) hydrogen bonds : angle 4.61125 ( 862) metal coordination : bond 0.01812 ( 4) metal coordination : angle 3.65352 ( 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 58 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8199 (t-90) REVERT: A 41 ARG cc_start: 0.8672 (mtm-85) cc_final: 0.8349 (mtm-85) REVERT: A 120 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7510 (ttp80) REVERT: A 334 LYS cc_start: 0.8884 (tptt) cc_final: 0.8632 (tppt) REVERT: A 505 TRP cc_start: 0.9218 (OUTLIER) cc_final: 0.8923 (m-10) REVERT: A 532 GLU cc_start: 0.8390 (tp30) cc_final: 0.8112 (tp30) REVERT: A 558 ARG cc_start: 0.7978 (ptt180) cc_final: 0.7496 (ptt180) REVERT: A 577 LEU cc_start: 0.8954 (mm) cc_final: 0.8559 (tp) outliers start: 11 outliers final: 6 residues processed: 56 average time/residue: 0.1504 time to fit residues: 10.3336 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 : 0.222 ------------------------------------------------------------------------------- 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 439 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 803 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: 9.9990 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.099402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067154 restraints weight = 31318.022| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.11 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7434 Z= 0.210 Angle : 0.734 16.766 10581 Z= 0.356 Chirality : 0.040 0.246 1268 Planarity : 0.005 0.051 983 Dihedral : 23.495 165.430 2293 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.93 % Allowed : 15.09 % Favored : 82.98 % 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 aren not related in a simple way. whole: 0.04 (0.34), residues: 615 helix: 1.42 (0.30), residues: 288 sheet: -0.77 (0.54), residues: 88 loop : -1.39 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 120 TYR 0.011 0.002 TYR A 356 PHE 0.012 0.002 PHE A 203 TRP 0.006 0.001 TRP A 766 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 7430) covalent geometry : angle 0.73391 (10580) hydrogen bonds : bond 0.05688 ( 324) hydrogen bonds : angle 4.54221 ( 862) metal coordination : bond 0.01428 ( 4) metal coordination : angle 3.04269 ( 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: 10 poor density : 47 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.8171 (t-90) REVERT: A 41 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8361 (mtm-85) REVERT: A 90 ASP cc_start: 0.8686 (p0) cc_final: 0.8360 (p0) REVERT: A 505 TRP cc_start: 0.9220 (OUTLIER) cc_final: 0.8960 (m-10) REVERT: A 532 GLU cc_start: 0.8341 (tp30) cc_final: 0.8123 (tp30) REVERT: A 577 LEU cc_start: 0.8872 (mm) cc_final: 0.8530 (tp) REVERT: A 582 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7094 (ttp80) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.1618 time to fit residues: 11.0399 Evaluate side-chains 55 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 803 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 52 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.097901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.067598 restraints weight = 30241.693| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.51 r_work: 0.2872 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7434 Z= 0.186 Angle : 0.731 16.204 10581 Z= 0.352 Chirality : 0.039 0.236 1268 Planarity : 0.005 0.044 983 Dihedral : 23.395 165.316 2293 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 15.47 % Favored : 82.79 % 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 aren not related in a simple way. whole: 0.04 (0.34), residues: 615 helix: 1.40 (0.31), residues: 289 sheet: -0.74 (0.55), residues: 88 loop : -1.39 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 558 TYR 0.011 0.001 TYR A 356 PHE 0.011 0.002 PHE A 203 TRP 0.007 0.001 TRP A 803 HIS 0.004 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7430) covalent geometry : angle 0.73043 (10580) hydrogen bonds : bond 0.05487 ( 324) hydrogen bonds : angle 4.48329 ( 862) metal coordination : bond 0.01135 ( 4) metal coordination : angle 2.74191 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1897.80 seconds wall clock time: 33 minutes 16.59 seconds (1996.59 seconds total)