Starting phenix.real_space_refine on Tue Jan 14 15:09:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8p_61237/01_2025/9j8p_61237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8p_61237/01_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_61237/01_2025/9j8p_61237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8p_61237/01_2025/9j8p_61237.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8p_61237/01_2025/9j8p_61237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8p_61237/01_2025/9j8p_61237.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 4.31, per 1000 atoms: 0.61 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: 1.86 Conformation dependent library (CDL) restraints added in 746.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 34 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 40 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 21 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 18 " Number of angles added : 1 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 49.8% alpha, 12.2% beta 28 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 2.39 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: 2.47 Time building geometry restraints manager: 2.05 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: 0.100 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.370 ------------------------------------------------------------------------------- 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 : 0.006 0.038 7430 Z= 0.401 Angle : 0.900 9.265 10580 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.060 0.009 TRP A 803 HIS 0.013 0.002 HIS A 859 PHE 0.050 0.005 PHE A 855 TYR 0.010 0.001 TYR A 356 ARG 0.004 0.000 ARG A 778 *********************** 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 : 0.561 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: 0.3461 time to fit residues: 30.6901 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 : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 40.0000 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** A 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.101556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.069913 restraints weight = 29789.787| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.53 r_work: 0.2938 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7430 Z= 0.289 Angle : 0.649 10.299 10580 Z= 0.324 Chirality : 0.039 0.284 1268 Planarity : 0.004 0.037 983 Dihedral : 23.504 168.923 2293 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 8.51 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.33), residues: 615 helix: 1.65 (0.30), residues: 288 sheet: -0.60 (0.55), residues: 81 loop : -1.71 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 803 HIS 0.007 0.001 HIS A 860 PHE 0.019 0.002 PHE A 627 TYR 0.011 0.002 TYR A 356 ARG 0.008 0.001 ARG A 445 *********************** 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 67 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8850 (t80) cc_final: 0.8526 (t80) REVERT: A 471 TRP cc_start: 0.8476 (m-10) cc_final: 0.8096 (m-10) REVERT: A 577 LEU cc_start: 0.9035 (mt) cc_final: 0.8713 (tp) REVERT: A 804 LEU cc_start: 0.9765 (mt) cc_final: 0.9543 (mt) REVERT: A 832 PHE cc_start: 0.8590 (p90) cc_final: 0.8278 (p90) REVERT: A 858 LEU cc_start: 0.9693 (tp) cc_final: 0.9385 (mm) REVERT: A 863 GLN cc_start: 0.9594 (mt0) cc_final: 0.9378 (mm-40) outliers start: 9 outliers final: 3 residues processed: 65 average time/residue: 0.3336 time to fit residues: 26.5311 Evaluate side-chains 53 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 10.9990 chunk 65 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 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 565 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN ** 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 = 0.4071 r_free = 0.4071 target = 0.103635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.070784 restraints weight = 31343.781| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.28 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7430 Z= 0.189 Angle : 0.573 9.636 10580 Z= 0.288 Chirality : 0.036 0.270 1268 Planarity : 0.004 0.034 983 Dihedral : 23.377 167.820 2293 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.35 % Allowed : 10.06 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.34), residues: 615 helix: 2.04 (0.30), residues: 290 sheet: -0.60 (0.56), residues: 81 loop : -1.57 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 531 HIS 0.003 0.001 HIS A 549 PHE 0.013 0.001 PHE A 627 TYR 0.009 0.001 TYR A 356 ARG 0.004 0.000 ARG A 585 *********************** 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 65 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.667 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: 0.8315 (OUTLIER) cc_final: 0.7839 (t-90) REVERT: A 59 PHE cc_start: 0.8613 (t80) cc_final: 0.8212 (t80) REVERT: A 90 ASP cc_start: 0.8319 (p0) cc_final: 0.7992 (p0) REVERT: A 116 LEU cc_start: 0.8841 (tt) cc_final: 0.8585 (tp) REVERT: A 471 TRP cc_start: 0.8175 (m-10) cc_final: 0.7819 (m-10) REVERT: A 532 GLU cc_start: 0.8334 (tp30) cc_final: 0.7940 (tp30) REVERT: A 625 GLN cc_start: 0.9390 (tp40) cc_final: 0.9182 (tm-30) REVERT: A 813 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8889 (mm-30) REVERT: A 858 LEU cc_start: 0.9666 (tp) cc_final: 0.9313 (mm) outliers start: 7 outliers final: 2 residues processed: 63 average time/residue: 0.3220 time to fit residues: 24.7889 Evaluate side-chains 52 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN A 625 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.099059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066445 restraints weight = 31268.075| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.16 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 7430 Z= 0.430 Angle : 0.739 8.903 10580 Z= 0.371 Chirality : 0.042 0.298 1268 Planarity : 0.005 0.057 983 Dihedral : 23.740 167.924 2293 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.29 % Allowed : 10.83 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.33), residues: 615 helix: 1.55 (0.30), residues: 285 sheet: -0.73 (0.56), residues: 83 loop : -1.45 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 803 HIS 0.008 0.001 HIS A 114 PHE 0.014 0.002 PHE A 203 TYR 0.015 0.002 TYR A 356 ARG 0.006 0.001 ARG A 558 *********************** 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 69 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.581 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: 0.8539 (OUTLIER) cc_final: 0.8080 (t-90) REVERT: A 41 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8438 (mtm-85) REVERT: A 505 TRP cc_start: 0.9278 (OUTLIER) cc_final: 0.8857 (m-10) REVERT: A 813 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8906 (mm-30) REVERT: A 849 GLN cc_start: 0.7221 (tt0) cc_final: 0.6977 (pt0) REVERT: A 858 LEU cc_start: 0.9622 (tp) cc_final: 0.9392 (mt) REVERT: A 859 HIS cc_start: 0.9108 (t-90) cc_final: 0.8858 (t-90) outliers start: 17 outliers final: 5 residues processed: 65 average time/residue: 0.3428 time to fit residues: 27.0763 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 : 0.571 ------------------------------------------------------------------------------- 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 803 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.100376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.069182 restraints weight = 29734.820| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.51 r_work: 0.2948 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7430 Z= 0.174 Angle : 0.601 10.284 10580 Z= 0.301 Chirality : 0.037 0.268 1268 Planarity : 0.004 0.034 983 Dihedral : 23.445 166.203 2293 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.55 % Allowed : 11.80 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.34), residues: 615 helix: 1.86 (0.30), residues: 289 sheet: -0.71 (0.55), residues: 86 loop : -1.42 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 531 HIS 0.003 0.001 HIS A 549 PHE 0.010 0.001 PHE A 832 TYR 0.009 0.001 TYR A 356 ARG 0.007 0.000 ARG A 558 *********************** 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: 8 poor density : 53 time to evaluate : 0.580 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: 0.8801 (OUTLIER) cc_final: 0.8358 (t-90) REVERT: A 59 PHE cc_start: 0.8831 (t80) cc_final: 0.8375 (t80) REVERT: A 334 LYS cc_start: 0.8787 (tptt) cc_final: 0.8514 (tppt) REVERT: A 505 TRP cc_start: 0.9304 (OUTLIER) cc_final: 0.9023 (m-10) REVERT: A 532 GLU cc_start: 0.8824 (tp30) cc_final: 0.8369 (tp30) REVERT: A 625 GLN cc_start: 0.9415 (tm-30) cc_final: 0.9086 (tm-30) REVERT: A 814 LEU cc_start: 0.9134 (mt) cc_final: 0.8887 (mt) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.3342 time to fit residues: 24.3656 Evaluate side-chains 56 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS 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 21 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** 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 = 0.4043 r_free = 0.4043 target = 0.101887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.069578 restraints weight = 30894.193| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.00 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7430 Z= 0.211 Angle : 0.649 16.039 10580 Z= 0.315 Chirality : 0.037 0.267 1268 Planarity : 0.004 0.035 983 Dihedral : 23.378 166.515 2293 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.71 % Allowed : 11.41 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.34), residues: 615 helix: 1.74 (0.31), residues: 295 sheet: -0.61 (0.55), residues: 86 loop : -1.31 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 531 HIS 0.003 0.001 HIS A 549 PHE 0.009 0.001 PHE A 203 TYR 0.010 0.001 TYR A 356 ARG 0.011 0.001 ARG A 628 *********************** 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 64 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8445 (OUTLIER) cc_final: 0.8015 (t-90) REVERT: A 41 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8302 (mtm-85) REVERT: A 90 ASP cc_start: 0.8868 (p0) cc_final: 0.8417 (p0) REVERT: A 471 TRP cc_start: 0.8251 (m-10) cc_final: 0.7864 (m-10) REVERT: A 505 TRP cc_start: 0.9221 (OUTLIER) cc_final: 0.8921 (m-10) REVERT: A 532 GLU cc_start: 0.8207 (tp30) cc_final: 0.7963 (tp30) outliers start: 14 outliers final: 6 residues processed: 62 average time/residue: 0.3099 time to fit residues: 23.4677 Evaluate side-chains 57 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 A 849 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.102448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070416 restraints weight = 30904.894| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.91 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7430 Z= 0.196 Angle : 0.646 15.487 10580 Z= 0.313 Chirality : 0.037 0.253 1268 Planarity : 0.004 0.038 983 Dihedral : 23.282 166.250 2293 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.93 % Allowed : 13.54 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.34), residues: 615 helix: 1.70 (0.30), residues: 294 sheet: -0.56 (0.54), residues: 86 loop : -1.30 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 531 HIS 0.003 0.001 HIS A 872 PHE 0.014 0.001 PHE A 59 TYR 0.009 0.001 TYR A 356 ARG 0.007 0.000 ARG A 558 *********************** 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: 10 poor density : 52 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.7971 (t-90) REVERT: A 41 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8324 (mtm-85) REVERT: A 505 TRP cc_start: 0.9207 (OUTLIER) cc_final: 0.8956 (m-10) REVERT: A 532 GLU cc_start: 0.8142 (tp30) cc_final: 0.7905 (tp30) REVERT: A 577 LEU cc_start: 0.8525 (tp) cc_final: 0.8316 (tp) REVERT: A 625 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8513 (pp30) outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.3495 time to fit residues: 25.0537 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 : 0.634 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** 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 = 0.4050 r_free = 0.4050 target = 0.102224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069565 restraints weight = 31275.350| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.06 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7430 Z= 0.209 Angle : 0.670 16.984 10580 Z= 0.325 Chirality : 0.037 0.245 1268 Planarity : 0.004 0.051 983 Dihedral : 23.256 166.342 2293 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 14.89 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.34), residues: 615 helix: 1.63 (0.30), residues: 296 sheet: -0.52 (0.55), residues: 86 loop : -1.25 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 531 HIS 0.003 0.001 HIS A 147 PHE 0.009 0.001 PHE A 203 TYR 0.010 0.001 TYR A 356 ARG 0.009 0.000 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8567 (OUTLIER) cc_final: 0.8098 (t-90) REVERT: A 41 ARG cc_start: 0.8547 (mtm-85) cc_final: 0.8304 (mtm-85) REVERT: A 59 PHE cc_start: 0.8730 (t80) cc_final: 0.8405 (t80) REVERT: A 90 ASP cc_start: 0.8878 (p0) cc_final: 0.7798 (p0) REVERT: A 505 TRP cc_start: 0.9209 (OUTLIER) cc_final: 0.8964 (m-10) REVERT: A 532 GLU cc_start: 0.8197 (tp30) cc_final: 0.7940 (tp30) REVERT: A 558 ARG cc_start: 0.7770 (ptt180) cc_final: 0.7421 (ptt180) REVERT: A 577 LEU cc_start: 0.8598 (tp) cc_final: 0.8336 (tp) outliers start: 9 outliers final: 6 residues processed: 56 average time/residue: 0.3164 time to fit residues: 21.6691 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 : 0.664 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 0.0470 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 2.5682 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.099836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.068323 restraints weight = 30093.036| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.51 r_work: 0.2931 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7430 Z= 0.227 Angle : 0.686 17.453 10580 Z= 0.329 Chirality : 0.038 0.245 1268 Planarity : 0.005 0.048 983 Dihedral : 23.274 166.287 2293 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.55 % Allowed : 15.86 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.34), residues: 615 helix: 1.63 (0.30), residues: 296 sheet: -0.58 (0.55), residues: 86 loop : -1.25 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 803 HIS 0.003 0.001 HIS A 549 PHE 0.009 0.001 PHE A 203 TYR 0.010 0.001 TYR A 356 ARG 0.006 0.000 ARG A 558 *********************** 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 59 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.568 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: 0.8885 (OUTLIER) cc_final: 0.8411 (t-90) REVERT: A 41 ARG cc_start: 0.8859 (mtm-85) cc_final: 0.8646 (mtm-85) REVERT: A 505 TRP cc_start: 0.9311 (OUTLIER) cc_final: 0.9064 (m-10) REVERT: A 532 GLU cc_start: 0.8714 (tp30) cc_final: 0.8257 (tp30) REVERT: A 577 LEU cc_start: 0.9024 (tp) cc_final: 0.8812 (tp) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 0.3248 time to fit residues: 22.5659 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 : 0.575 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 54 optimal weight: 40.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** 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 = 0.4049 r_free = 0.4049 target = 0.101263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070101 restraints weight = 30686.532| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.55 r_work: 0.2980 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7430 Z= 0.174 Angle : 0.666 18.349 10580 Z= 0.320 Chirality : 0.036 0.233 1268 Planarity : 0.004 0.047 983 Dihedral : 23.157 165.853 2293 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.55 % Allowed : 15.09 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.35), residues: 615 helix: 1.77 (0.31), residues: 296 sheet: -0.44 (0.55), residues: 87 loop : -1.32 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 531 HIS 0.002 0.001 HIS A 549 PHE 0.010 0.001 PHE A 832 TYR 0.008 0.001 TYR A 356 ARG 0.008 0.000 ARG A 120 ********************** 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 60 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.571 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: 0.8878 (OUTLIER) cc_final: 0.8424 (t-90) REVERT: A 59 PHE cc_start: 0.8826 (t80) cc_final: 0.8618 (t80) REVERT: A 90 ASP cc_start: 0.8972 (p0) cc_final: 0.8243 (p0) REVERT: A 120 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7691 (ttp80) REVERT: A 471 TRP cc_start: 0.8449 (m-10) cc_final: 0.8053 (m-10) REVERT: A 532 GLU cc_start: 0.8763 (tp30) cc_final: 0.8309 (tp30) REVERT: A 577 LEU cc_start: 0.9074 (tp) cc_final: 0.8852 (tp) REVERT: A 582 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7726 (tmm-80) REVERT: A 842 MET cc_start: 0.6201 (tmm) cc_final: 0.5884 (tmm) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.3288 time to fit residues: 23.1726 Evaluate side-chains 56 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 468 VAL 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 28 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4046 r_free = 0.4046 target = 0.101223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069913 restraints weight = 29739.317| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.51 r_work: 0.2977 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7430 Z= 0.177 Angle : 0.655 17.658 10580 Z= 0.317 Chirality : 0.036 0.231 1268 Planarity : 0.004 0.044 983 Dihedral : 23.104 166.100 2293 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.55 % Allowed : 15.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.35), residues: 615 helix: 1.77 (0.31), residues: 298 sheet: -0.41 (0.55), residues: 87 loop : -1.24 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 531 HIS 0.002 0.001 HIS A 549 PHE 0.009 0.001 PHE A 832 TYR 0.008 0.001 TYR A 356 ARG 0.010 0.001 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3645.14 seconds wall clock time: 66 minutes 34.86 seconds (3994.86 seconds total)