Starting phenix.real_space_refine on Tue Mar 11 23:12:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8p_61237/03_2025/9j8p_61237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8p_61237/03_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_61237/03_2025/9j8p_61237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8p_61237/03_2025/9j8p_61237.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8p_61237/03_2025/9j8p_61237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8p_61237/03_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-5624/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: 4.61, per 1000 atoms: 0.65 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: 1.71 Conformation dependent library (CDL) restraints added in 877.6 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: 2.53 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: 2.84 Time building geometry restraints manager: 2.06 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: 0.150 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- 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 : 0.537 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: 0.3322 time to fit residues: 29.5086 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 : 0.575 ------------------------------------------------------------------------------- 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: 4.60 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.636 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: 0.8851 (t80) cc_final: 0.8526 (t80) REVERT: A 471 TRP cc_start: 0.8474 (m-10) cc_final: 0.8093 (m-10) REVERT: A 577 LEU cc_start: 0.9038 (mt) cc_final: 0.8714 (tp) REVERT: A 804 LEU cc_start: 0.9763 (mt) cc_final: 0.9541 (mt) REVERT: A 832 PHE cc_start: 0.8592 (p90) cc_final: 0.8281 (p90) REVERT: A 858 LEU cc_start: 0.9692 (tp) cc_final: 0.9384 (mm) REVERT: A 863 GLN cc_start: 0.9598 (mt0) cc_final: 0.9381 (mm-40) outliers start: 9 outliers final: 3 residues processed: 65 average time/residue: 0.3375 time to fit residues: 27.0624 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 : 0.625 ------------------------------------------------------------------------------- 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: 8.9990 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: 10.0000 chunk 41 optimal weight: 4.9990 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 = 0.070773 restraints weight = 31343.143| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.27 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 9.635 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 0.012 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 : 0.583 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: 0.8292 (OUTLIER) cc_final: 0.7822 (t-90) REVERT: A 59 PHE cc_start: 0.8606 (t80) cc_final: 0.8211 (t80) REVERT: A 90 ASP cc_start: 0.8312 (p0) cc_final: 0.7984 (p0) REVERT: A 116 LEU cc_start: 0.8838 (tt) cc_final: 0.8585 (tp) REVERT: A 471 TRP cc_start: 0.8165 (m-10) cc_final: 0.7817 (m-10) REVERT: A 532 GLU cc_start: 0.8316 (tp30) cc_final: 0.7933 (tp30) REVERT: A 625 GLN cc_start: 0.9384 (tp40) cc_final: 0.9177 (tm-30) REVERT: A 813 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8887 (mm-30) REVERT: A 858 LEU cc_start: 0.9664 (tp) cc_final: 0.9313 (mm) outliers start: 7 outliers final: 2 residues processed: 63 average time/residue: 0.3042 time to fit residues: 23.5310 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 : 0.558 ------------------------------------------------------------------------------- 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: 8.9990 chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 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: 0.0970 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.101069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068614 restraints weight = 31246.584| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.14 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7430 Z= 0.302 Angle : 0.648 8.765 10580 Z= 0.325 Chirality : 0.039 0.284 1268 Planarity : 0.004 0.032 983 Dihedral : 23.512 167.698 2293 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.71 % Allowed : 11.22 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.34), residues: 615 helix: 1.88 (0.30), residues: 288 sheet: -0.64 (0.54), residues: 86 loop : -1.42 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 803 HIS 0.006 0.001 HIS A 114 PHE 0.012 0.002 PHE A 203 TYR 0.013 0.002 TYR A 356 ARG 0.005 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 66 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8016 (t-90) REVERT: A 90 ASP cc_start: 0.8725 (p0) cc_final: 0.8449 (p0) REVERT: A 471 TRP cc_start: 0.8248 (m-10) cc_final: 0.7830 (m-10) REVERT: A 505 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.8972 (m-10) REVERT: A 532 GLU cc_start: 0.8196 (tp30) cc_final: 0.7954 (tp30) REVERT: A 577 LEU cc_start: 0.8874 (mm) cc_final: 0.8551 (tp) REVERT: A 813 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8869 (mm-30) REVERT: A 858 LEU cc_start: 0.9616 (tp) cc_final: 0.9366 (mt) REVERT: A 859 HIS cc_start: 0.9081 (t-90) cc_final: 0.8840 (t-90) outliers start: 14 outliers final: 4 residues processed: 63 average time/residue: 0.3360 time to fit residues: 25.8478 Evaluate side-chains 52 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 812 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.101478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.070968 restraints weight = 29784.742| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.68 r_work: 0.2963 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7430 Z= 0.159 Angle : 0.577 9.841 10580 Z= 0.289 Chirality : 0.036 0.265 1268 Planarity : 0.004 0.032 983 Dihedral : 23.314 166.537 2293 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.93 % Allowed : 11.80 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.97 (0.30), residues: 290 sheet: -0.90 (0.51), residues: 98 loop : -1.35 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 531 HIS 0.004 0.001 HIS A 859 PHE 0.011 0.001 PHE A 832 TYR 0.008 0.001 TYR A 356 ARG 0.006 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 66 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.570 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: 0.8871 (OUTLIER) cc_final: 0.8404 (t-90) REVERT: A 41 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8690 (mtm-85) REVERT: A 59 PHE cc_start: 0.8852 (t80) cc_final: 0.8394 (t80) REVERT: A 471 TRP cc_start: 0.8469 (m-10) cc_final: 0.8083 (m-10) REVERT: A 505 TRP cc_start: 0.9278 (OUTLIER) cc_final: 0.9039 (m-10) REVERT: A 532 GLU cc_start: 0.8828 (tp30) cc_final: 0.8317 (tp30) REVERT: A 577 LEU cc_start: 0.9045 (mm) cc_final: 0.8672 (tp) REVERT: A 582 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7728 (ttp80) outliers start: 10 outliers final: 3 residues processed: 65 average time/residue: 0.3100 time to fit residues: 24.5642 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 : 0.615 ------------------------------------------------------------------------------- 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 468 VAL Chi-restraints excluded: chain A residue 505 TRP 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: 0.9990 chunk 62 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4038 r_free = 0.4038 target = 0.101712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069479 restraints weight = 31031.646| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.92 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7430 Z= 0.237 Angle : 0.658 16.448 10580 Z= 0.319 Chirality : 0.038 0.273 1268 Planarity : 0.004 0.047 983 Dihedral : 23.337 166.983 2293 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.93 % Allowed : 12.57 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.34), residues: 615 helix: 1.77 (0.30), residues: 289 sheet: -0.58 (0.55), residues: 86 loop : -1.30 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 803 HIS 0.003 0.001 HIS A 859 PHE 0.010 0.002 PHE A 203 TYR 0.011 0.002 TYR A 75 ARG 0.009 0.000 ARG A 558 *********************** 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 62 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.7993 (t-90) REVERT: A 41 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8380 (mtm-85) REVERT: A 90 ASP cc_start: 0.8810 (p0) cc_final: 0.8276 (p0) REVERT: A 116 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 505 TRP cc_start: 0.9225 (OUTLIER) cc_final: 0.8948 (m-10) REVERT: A 532 GLU cc_start: 0.8077 (tp30) cc_final: 0.7869 (tp30) REVERT: A 577 LEU cc_start: 0.8827 (mm) cc_final: 0.8512 (tp) REVERT: A 582 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7215 (ttp80) outliers start: 10 outliers final: 5 residues processed: 60 average time/residue: 0.3263 time to fit residues: 23.7554 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 : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 116 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 0.0770 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 0.0020 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8148 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.102289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.071233 restraints weight = 30067.617| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.53 r_work: 0.3016 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7430 Z= 0.146 Angle : 0.610 16.223 10580 Z= 0.296 Chirality : 0.036 0.251 1268 Planarity : 0.004 0.046 983 Dihedral : 23.164 166.161 2293 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.74 % Allowed : 12.38 % 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: 0.51 (0.34), residues: 615 helix: 1.81 (0.31), residues: 296 sheet: -0.29 (0.55), residues: 86 loop : -1.38 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 531 HIS 0.002 0.000 HIS A 549 PHE 0.011 0.001 PHE A 832 TYR 0.007 0.001 TYR A 356 ARG 0.006 0.000 ARG A 120 *********************** 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 60 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8528 (t70) REVERT: A 59 PHE cc_start: 0.8780 (t80) cc_final: 0.8230 (t80) REVERT: A 90 ASP cc_start: 0.8950 (p0) cc_final: 0.8670 (p0) REVERT: A 471 TRP cc_start: 0.8410 (m-10) cc_final: 0.8007 (m-10) REVERT: A 532 GLU cc_start: 0.8815 (tp30) cc_final: 0.8311 (tp30) REVERT: A 577 LEU cc_start: 0.9058 (mm) cc_final: 0.8646 (tp) outliers start: 9 outliers final: 5 residues processed: 59 average time/residue: 0.3330 time to fit residues: 23.8108 Evaluate side-chains 54 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 72 LEU 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 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: 5.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.101210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066528 restraints weight = 31128.207| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.68 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7430 Z= 0.277 Angle : 0.677 16.138 10580 Z= 0.332 Chirality : 0.038 0.255 1268 Planarity : 0.005 0.044 983 Dihedral : 23.283 167.023 2293 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.55 % Allowed : 13.54 % Favored : 84.91 % 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: 0.31 (0.34), residues: 615 helix: 1.58 (0.30), residues: 289 sheet: -0.42 (0.56), residues: 86 loop : -1.28 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 589 HIS 0.006 0.001 HIS A 114 PHE 0.010 0.002 PHE A 475 TYR 0.013 0.002 TYR A 75 ARG 0.009 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.622 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: 0.8493 (OUTLIER) cc_final: 0.8053 (t-90) REVERT: A 471 TRP cc_start: 0.8207 (m-10) cc_final: 0.7791 (m-10) REVERT: A 532 GLU cc_start: 0.8157 (tp30) cc_final: 0.7948 (tp30) REVERT: A 558 ARG cc_start: 0.7993 (ptt180) cc_final: 0.7421 (ptt180) REVERT: A 577 LEU cc_start: 0.8786 (mm) cc_final: 0.8504 (tp) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 0.3417 time to fit residues: 23.9460 Evaluate side-chains 57 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 72 LEU 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 627 PHE Chi-restraints excluded: chain A residue 787 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.099991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.067591 restraints weight = 31183.777| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.04 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7430 Z= 0.315 Angle : 0.721 17.385 10580 Z= 0.351 Chirality : 0.040 0.256 1268 Planarity : 0.005 0.044 983 Dihedral : 23.457 166.223 2293 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.13 % Allowed : 13.73 % Favored : 84.14 % 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: 0.06 (0.34), residues: 615 helix: 1.43 (0.30), residues: 289 sheet: -0.88 (0.52), residues: 88 loop : -1.34 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 589 HIS 0.003 0.001 HIS A 549 PHE 0.012 0.002 PHE A 63 TYR 0.011 0.002 TYR A 356 ARG 0.007 0.001 ARG A 120 *********************** 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 61 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.565 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: 0.8577 (OUTLIER) cc_final: 0.8118 (t-90) REVERT: A 65 ARG cc_start: 0.8491 (tpm170) cc_final: 0.8222 (tpm170) REVERT: A 120 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7570 (ttp80) REVERT: A 532 GLU cc_start: 0.8228 (tp30) cc_final: 0.7982 (tp30) REVERT: A 558 ARG cc_start: 0.7829 (ptt180) cc_final: 0.7508 (ptt180) REVERT: A 577 LEU cc_start: 0.8846 (mm) cc_final: 0.8479 (tp) outliers start: 11 outliers final: 8 residues processed: 58 average time/residue: 0.3152 time to fit residues: 22.3498 Evaluate side-chains 59 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 72 LEU 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 627 PHE 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: 0.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 13 optimal weight: 0.1980 chunk 48 optimal weight: 0.0470 chunk 66 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.2484 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.100719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.070315 restraints weight = 30610.036| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.61 r_work: 0.2960 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7430 Z= 0.165 Angle : 0.661 17.834 10580 Z= 0.319 Chirality : 0.037 0.231 1268 Planarity : 0.004 0.041 983 Dihedral : 23.241 165.318 2293 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.35 % Allowed : 14.51 % Favored : 84.14 % 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: 0.25 (0.34), residues: 615 helix: 1.68 (0.31), residues: 292 sheet: -0.69 (0.55), residues: 89 loop : -1.46 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 531 HIS 0.003 0.001 HIS A 549 PHE 0.012 0.001 PHE A 832 TYR 0.008 0.001 TYR A 356 ARG 0.007 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 57 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8475 (t-90) REVERT: A 41 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8629 (mtm-85) REVERT: A 65 ARG cc_start: 0.8676 (tpm170) cc_final: 0.8336 (tpm170) REVERT: A 532 GLU cc_start: 0.8850 (tp30) cc_final: 0.8354 (tp30) REVERT: A 558 ARG cc_start: 0.8742 (ptt180) cc_final: 0.8445 (ptt180) REVERT: A 577 LEU cc_start: 0.9026 (mm) cc_final: 0.8643 (tp) REVERT: A 582 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7661 (tmm-80) REVERT: A 625 GLN cc_start: 0.9486 (tm-30) cc_final: 0.9241 (pp30) REVERT: A 842 MET cc_start: 0.6365 (tmm) cc_final: 0.6044 (tmm) REVERT: A 854 LEU cc_start: 0.9653 (mm) cc_final: 0.9031 (tt) REVERT: A 858 LEU cc_start: 0.9354 (pt) cc_final: 0.9152 (pt) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.3406 time to fit residues: 23.0324 Evaluate side-chains 55 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 72 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 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: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.101458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068820 restraints weight = 30880.842| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.29 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7430 Z= 0.227 Angle : 0.678 17.644 10580 Z= 0.328 Chirality : 0.038 0.235 1268 Planarity : 0.004 0.044 983 Dihedral : 23.243 165.942 2293 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.16 % Allowed : 14.89 % Favored : 83.95 % 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: 0.22 (0.34), residues: 615 helix: 1.56 (0.31), residues: 298 sheet: -0.73 (0.55), residues: 88 loop : -1.40 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 531 HIS 0.003 0.001 HIS A 114 PHE 0.009 0.001 PHE A 832 TYR 0.010 0.001 TYR A 356 ARG 0.009 0.000 ARG A 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3801.14 seconds wall clock time: 65 minutes 48.00 seconds (3948.00 seconds total)