Starting phenix.real_space_refine on Tue Jan 14 04:56:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcc_38239/01_2025/8xcc_38239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcc_38239/01_2025/8xcc_38239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcc_38239/01_2025/8xcc_38239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcc_38239/01_2025/8xcc_38239.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcc_38239/01_2025/8xcc_38239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcc_38239/01_2025/8xcc_38239.cif" } resolution = 3.2 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= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 21 5.16 5 C 3332 2.51 5 N 1034 2.21 5 O 1174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 5617 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4435 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 17, 'TRANS': 528} Chain breaks: 7 Chain: "B" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 850 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 17, 'rna3p_pyr': 19} Link IDs: {'rna2p': 4, 'rna3p': 35} Chain: "C" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 4.71, per 1000 atoms: 0.84 Number of scatterers: 5617 At special positions: 0 Unit cell: (91.08, 72.6, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 56 15.00 O 1174 8.00 N 1034 7.00 C 3332 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: 1.70 Conformation dependent library (CDL) restraints added in 700.1 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 53.3% alpha, 19.2% beta 23 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.569A pdb=" N ARG A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.648A pdb=" N THR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.657A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 211 through 238 Processing helix chain 'A' and resid 387 through 391 removed outlier: 4.059A pdb=" N TRP A 391 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 552 removed outlier: 3.912A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.542A pdb=" N LYS A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 578 through 606 removed outlier: 3.640A pdb=" N ARG A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 621 through 642 removed outlier: 3.538A pdb=" N ARG A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 689 Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.696A pdb=" N LEU A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 737 Processing helix chain 'A' and resid 784 through 797 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 11 removed outlier: 4.162A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 11 removed outlier: 4.162A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 517 removed outlier: 3.704A pdb=" N SER A 513 " --> pdb=" O VAL A 489 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.94 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: 1327 1.33 - 1.45: 1427 1.45 - 1.57: 2937 1.57 - 1.69: 109 1.69 - 1.81: 33 Bond restraints: 5833 Sorted by residual: bond pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 1.516 1.508 0.008 8.90e-03 1.26e+04 7.50e-01 bond pdb=" C3' DG C 7 " pdb=" C2' DG C 7 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.00e-02 2.50e+03 7.36e-01 bond pdb=" O4' DT C 5 " pdb=" C1' DT C 5 " ideal model delta sigma weight residual 1.414 1.397 0.017 2.00e-02 2.50e+03 7.13e-01 bond pdb=" O4' DT C 3 " pdb=" C1' DT C 3 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.95e-01 bond pdb=" CA ASP A 238 " pdb=" C ASP A 238 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.72e-02 3.38e+03 5.85e-01 ... (remaining 5828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 7930 1.70 - 3.41: 159 3.41 - 5.11: 16 5.11 - 6.82: 3 6.82 - 8.52: 2 Bond angle restraints: 8110 Sorted by residual: angle pdb=" N PHE A 202 " pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 109.81 115.82 -6.01 2.21e+00 2.05e-01 7.39e+00 angle pdb=" CA LEU A 516 " pdb=" CB LEU A 516 " pdb=" CG LEU A 516 " ideal model delta sigma weight residual 116.30 124.82 -8.52 3.50e+00 8.16e-02 5.93e+00 angle pdb=" N ILE A 481 " pdb=" CA ILE A 481 " pdb=" C ILE A 481 " ideal model delta sigma weight residual 111.90 110.09 1.81 8.10e-01 1.52e+00 4.97e+00 angle pdb=" CA LEU A 362 " pdb=" CB LEU A 362 " pdb=" CG LEU A 362 " ideal model delta sigma weight residual 116.30 123.45 -7.15 3.50e+00 8.16e-02 4.17e+00 angle pdb=" C THR A 514 " pdb=" N GLY A 515 " pdb=" CA GLY A 515 " ideal model delta sigma weight residual 121.03 118.03 3.00 1.51e+00 4.39e-01 3.94e+00 ... (remaining 8105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 3356 34.93 - 69.87: 189 69.87 - 104.80: 21 104.80 - 139.74: 1 139.74 - 174.67: 1 Dihedral angle restraints: 3568 sinusoidal: 1976 harmonic: 1592 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 46.67 -174.67 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA PHE A 571 " pdb=" C PHE A 571 " pdb=" N ARG A 572 " pdb=" CA ARG A 572 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" O4' A B -21 " pdb=" C1' A B -21 " pdb=" N9 A B -21 " pdb=" C4 A B -21 " ideal model delta sinusoidal sigma weight residual -90.00 -14.24 -75.76 1 2.00e+01 2.50e-03 1.81e+01 ... (remaining 3565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 610 0.028 - 0.056: 213 0.056 - 0.084: 63 0.084 - 0.113: 30 0.113 - 0.141: 9 Chirality restraints: 925 Sorted by residual: chirality pdb=" CA PHE A 202 " pdb=" N PHE A 202 " pdb=" C PHE A 202 " pdb=" CB PHE A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE A 573 " pdb=" N ILE A 573 " pdb=" C ILE A 573 " pdb=" CB ILE A 573 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 922 not shown) Planarity restraints: 835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B -35 " -0.021 2.00e-02 2.50e+03 1.10e-02 2.74e+00 pdb=" N1 U B -35 " 0.024 2.00e-02 2.50e+03 pdb=" C2 U B -35 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U B -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U B -35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B -35 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B -35 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U B -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U B -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -36 " -0.020 2.00e-02 2.50e+03 8.65e-03 2.24e+00 pdb=" N9 G B -36 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G B -36 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B -36 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B -36 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B -36 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B -36 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B -36 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B -36 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B -36 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B -36 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B -36 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 482 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 483 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " 0.019 5.00e-02 4.00e+02 ... (remaining 832 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 513 2.74 - 3.28: 5397 3.28 - 3.82: 9880 3.82 - 4.36: 11174 4.36 - 4.90: 18481 Nonbonded interactions: 45445 Sorted by model distance: nonbonded pdb=" OH TYR A 389 " pdb=" OP2 C B 0 " model vdw 2.197 3.040 nonbonded pdb=" O2' C B 0 " pdb=" O5' U B 1 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 666 " pdb=" OP2 U B -32 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU A 111 " pdb=" NZ LYS A 112 " model vdw 2.297 3.120 nonbonded pdb=" O LEU A 110 " pdb=" NH2 ARG A 197 " model vdw 2.311 3.120 ... (remaining 45440 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 : 0.004 0.024 5833 Z= 0.229 Angle : 0.583 8.523 8110 Z= 0.317 Chirality : 0.036 0.141 925 Planarity : 0.003 0.034 835 Dihedral : 19.549 174.670 2536 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.21 % Allowed : 11.42 % Favored : 88.37 % 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: 1.81 (0.38), residues: 530 helix: 2.54 (0.32), residues: 257 sheet: 0.71 (0.52), residues: 92 loop : -0.54 (0.51), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 229 HIS 0.002 0.001 HIS A 609 PHE 0.013 0.001 PHE A 202 TYR 0.009 0.001 TYR A 22 ARG 0.004 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.627 Fit side-chains REVERT: A 420 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8382 (tt0) REVERT: A 696 MET cc_start: 0.8900 (ptp) cc_final: 0.8639 (ptt) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1936 time to fit residues: 9.8617 Evaluate side-chains 34 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.075083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.059842 restraints weight = 14973.326| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.83 r_work: 0.2742 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5833 Z= 0.227 Angle : 0.539 7.654 8110 Z= 0.285 Chirality : 0.037 0.170 925 Planarity : 0.004 0.034 835 Dihedral : 20.565 174.193 1433 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.11 % Allowed : 12.05 % Favored : 85.84 % 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: 2.25 (0.38), residues: 530 helix: 2.79 (0.31), residues: 268 sheet: 0.42 (0.49), residues: 95 loop : 0.00 (0.54), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.004 0.001 HIS A 609 PHE 0.009 0.001 PHE A 390 TYR 0.012 0.001 TYR A 44 ARG 0.005 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.540 Fit side-chains REVERT: A 48 MET cc_start: 0.8707 (mpp) cc_final: 0.8096 (mpp) REVERT: A 102 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8777 (mp0) REVERT: A 202 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7309 (t80) REVERT: A 420 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8495 (tt0) REVERT: A 797 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6240 (ptp-170) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 0.1502 time to fit residues: 9.3871 Evaluate side-chains 44 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.058355 restraints weight = 15084.030| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.83 r_work: 0.2709 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5833 Z= 0.311 Angle : 0.564 7.623 8110 Z= 0.296 Chirality : 0.038 0.198 925 Planarity : 0.004 0.031 835 Dihedral : 20.517 174.362 1433 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.81 % Allowed : 11.42 % Favored : 84.78 % 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: 2.22 (0.38), residues: 530 helix: 2.82 (0.31), residues: 268 sheet: 0.34 (0.48), residues: 102 loop : -0.07 (0.56), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 229 HIS 0.005 0.001 HIS A 609 PHE 0.012 0.002 PHE A 390 TYR 0.010 0.001 TYR A 44 ARG 0.004 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.583 Fit side-chains REVERT: A 48 MET cc_start: 0.8675 (mpp) cc_final: 0.7991 (mpp) REVERT: A 70 CYS cc_start: 0.9305 (t) cc_final: 0.8341 (p) REVERT: A 102 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8680 (mp0) REVERT: A 202 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7264 (t80) REVERT: A 420 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8466 (tt0) REVERT: A 797 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6242 (ptm160) outliers start: 18 outliers final: 10 residues processed: 49 average time/residue: 0.1871 time to fit residues: 12.3333 Evaluate side-chains 47 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.059440 restraints weight = 15262.206| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.84 r_work: 0.2735 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5833 Z= 0.217 Angle : 0.524 8.170 8110 Z= 0.275 Chirality : 0.037 0.168 925 Planarity : 0.003 0.036 835 Dihedral : 20.467 173.926 1433 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.17 % Allowed : 12.68 % 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: 2.52 (0.38), residues: 530 helix: 3.11 (0.31), residues: 265 sheet: 0.41 (0.48), residues: 100 loop : 0.08 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 PHE 0.010 0.001 PHE A 390 TYR 0.009 0.001 TYR A 44 ARG 0.005 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8658 (mpp) cc_final: 0.7956 (mpp) REVERT: A 70 CYS cc_start: 0.9292 (t) cc_final: 0.8351 (p) REVERT: A 99 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9112 (tt) REVERT: A 202 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7325 (t80) REVERT: A 420 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8470 (tt0) REVERT: A 797 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6221 (ptm160) outliers start: 15 outliers final: 12 residues processed: 51 average time/residue: 0.1611 time to fit residues: 11.2670 Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.060731 restraints weight = 14848.865| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.84 r_work: 0.2765 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5833 Z= 0.173 Angle : 0.501 8.277 8110 Z= 0.264 Chirality : 0.036 0.150 925 Planarity : 0.003 0.037 835 Dihedral : 20.410 174.393 1433 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.17 % Allowed : 13.53 % Favored : 83.30 % 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: 2.57 (0.38), residues: 530 helix: 3.16 (0.31), residues: 265 sheet: 0.43 (0.48), residues: 100 loop : 0.08 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.002 0.001 HIS A 609 PHE 0.010 0.001 PHE A 390 TYR 0.008 0.001 TYR A 22 ARG 0.007 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8639 (mpp) cc_final: 0.7849 (mpp) REVERT: A 99 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9101 (tt) REVERT: A 202 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7227 (t80) REVERT: A 420 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8495 (tt0) REVERT: A 714 ASN cc_start: 0.7220 (OUTLIER) cc_final: 0.6206 (p0) REVERT: A 797 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6104 (ptp-170) outliers start: 15 outliers final: 10 residues processed: 49 average time/residue: 0.1641 time to fit residues: 11.1162 Evaluate side-chains 50 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 55 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.059928 restraints weight = 15152.249| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.92 r_work: 0.2750 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5833 Z= 0.205 Angle : 0.512 8.713 8110 Z= 0.267 Chirality : 0.036 0.160 925 Planarity : 0.003 0.040 835 Dihedral : 20.404 174.507 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.17 % Allowed : 13.95 % Favored : 82.88 % 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: 2.60 (0.38), residues: 530 helix: 3.20 (0.31), residues: 265 sheet: 0.42 (0.48), residues: 100 loop : 0.11 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 PHE 0.009 0.001 PHE A 390 TYR 0.009 0.001 TYR A 22 ARG 0.005 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8621 (mpp) cc_final: 0.7882 (mpp) REVERT: A 70 CYS cc_start: 0.9294 (t) cc_final: 0.8348 (p) REVERT: A 99 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9124 (tt) REVERT: A 202 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7244 (t80) REVERT: A 420 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8508 (tt0) REVERT: A 714 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6206 (p0) REVERT: A 797 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6148 (ptp-170) outliers start: 15 outliers final: 10 residues processed: 51 average time/residue: 0.1631 time to fit residues: 11.6529 Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.059608 restraints weight = 15076.793| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.86 r_work: 0.2745 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5833 Z= 0.218 Angle : 0.519 8.428 8110 Z= 0.270 Chirality : 0.036 0.165 925 Planarity : 0.003 0.038 835 Dihedral : 20.405 174.412 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.81 % Allowed : 13.74 % Favored : 82.45 % 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: 2.60 (0.38), residues: 530 helix: 3.21 (0.31), residues: 265 sheet: 0.35 (0.48), residues: 100 loop : 0.13 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 PHE 0.009 0.001 PHE A 390 TYR 0.009 0.001 TYR A 22 ARG 0.006 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8621 (mpp) cc_final: 0.7892 (mpp) REVERT: A 70 CYS cc_start: 0.9278 (t) cc_final: 0.8354 (p) REVERT: A 99 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9115 (tt) REVERT: A 202 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7314 (t80) REVERT: A 420 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8420 (tt0) REVERT: A 714 ASN cc_start: 0.7241 (OUTLIER) cc_final: 0.6184 (p0) REVERT: A 797 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6153 (ptp-170) outliers start: 18 outliers final: 10 residues processed: 53 average time/residue: 0.2008 time to fit residues: 14.1813 Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 42 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.075139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.059642 restraints weight = 14988.641| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.86 r_work: 0.2744 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5833 Z= 0.210 Angle : 0.517 8.328 8110 Z= 0.270 Chirality : 0.036 0.164 925 Planarity : 0.004 0.040 835 Dihedral : 20.405 174.377 1433 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.17 % Allowed : 14.16 % Favored : 82.66 % 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: 2.64 (0.39), residues: 530 helix: 3.24 (0.31), residues: 265 sheet: 0.37 (0.48), residues: 100 loop : 0.15 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 PHE 0.009 0.001 PHE A 390 TYR 0.009 0.001 TYR A 22 ARG 0.006 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8623 (mpp) cc_final: 0.7910 (mpp) REVERT: A 70 CYS cc_start: 0.9274 (t) cc_final: 0.8342 (p) REVERT: A 99 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9107 (tt) REVERT: A 202 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7299 (t80) REVERT: A 420 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8443 (tt0) REVERT: A 714 ASN cc_start: 0.7241 (OUTLIER) cc_final: 0.6173 (p0) REVERT: A 797 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6128 (ptp-170) outliers start: 15 outliers final: 11 residues processed: 50 average time/residue: 0.1680 time to fit residues: 11.7363 Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.060000 restraints weight = 15016.440| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.85 r_work: 0.2749 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5833 Z= 0.183 Angle : 0.509 8.515 8110 Z= 0.266 Chirality : 0.035 0.154 925 Planarity : 0.003 0.039 835 Dihedral : 20.400 174.312 1433 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.17 % Allowed : 14.16 % Favored : 82.66 % 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: 2.65 (0.39), residues: 530 helix: 3.26 (0.31), residues: 265 sheet: 0.39 (0.48), residues: 100 loop : 0.14 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.002 0.001 HIS A 609 PHE 0.009 0.001 PHE A 390 TYR 0.009 0.001 TYR A 22 ARG 0.007 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8629 (mpp) cc_final: 0.7911 (mpp) REVERT: A 99 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9100 (tt) REVERT: A 202 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7291 (t80) REVERT: A 420 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8438 (tt0) REVERT: A 714 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6183 (p0) REVERT: A 797 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6143 (ptp-170) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.1605 time to fit residues: 11.6158 Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.059380 restraints weight = 15237.050| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.89 r_work: 0.2733 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5833 Z= 0.225 Angle : 0.524 8.386 8110 Z= 0.273 Chirality : 0.036 0.166 925 Planarity : 0.004 0.040 835 Dihedral : 20.394 174.332 1433 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.17 % Allowed : 14.80 % Favored : 82.03 % 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: 2.65 (0.39), residues: 530 helix: 3.28 (0.31), residues: 265 sheet: 0.37 (0.48), residues: 100 loop : 0.09 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 PHE 0.009 0.001 PHE A 390 TYR 0.009 0.001 TYR A 22 ARG 0.007 0.000 ARG A 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8614 (mpp) cc_final: 0.7897 (mpp) REVERT: A 99 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9088 (tt) REVERT: A 202 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7285 (t80) REVERT: A 420 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8449 (tt0) REVERT: A 714 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6206 (p0) REVERT: A 797 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6156 (ptp-170) outliers start: 15 outliers final: 10 residues processed: 50 average time/residue: 0.1713 time to fit residues: 11.9948 Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 797 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.059218 restraints weight = 15223.185| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.90 r_work: 0.2731 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5833 Z= 0.237 Angle : 0.527 8.294 8110 Z= 0.275 Chirality : 0.036 0.170 925 Planarity : 0.004 0.038 835 Dihedral : 20.427 174.008 1433 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.17 % Allowed : 14.80 % Favored : 82.03 % 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: 2.62 (0.39), residues: 530 helix: 3.27 (0.31), residues: 265 sheet: 0.29 (0.48), residues: 100 loop : 0.11 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 PHE 0.010 0.001 PHE A 390 TYR 0.010 0.001 TYR A 22 ARG 0.007 0.000 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.97 seconds wall clock time: 44 minutes 19.63 seconds (2659.63 seconds total)