Starting phenix.real_space_refine on Thu Mar 6 09:08:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcc_38239/03_2025/8xcc_38239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcc_38239/03_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_38239/03_2025/8xcc_38239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcc_38239/03_2025/8xcc_38239.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcc_38239/03_2025/8xcc_38239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcc_38239/03_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-5624/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: 4.86, per 1000 atoms: 0.87 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: 1.74 Conformation dependent library (CDL) restraints added in 603.3 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: 1.89 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: 1.93 Time building geometry restraints manager: 1.76 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: 4.330 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 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 : 0.520 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: 0.1733 time to fit residues: 8.8430 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 : 0.511 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.075592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.060387 restraints weight = 14937.102| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.83 r_work: 0.2756 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0667 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= 0.195 Angle : 0.526 7.803 8110 Z= 0.278 Chirality : 0.037 0.168 925 Planarity : 0.003 0.035 835 Dihedral : 20.549 174.201 1433 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.11 % Allowed : 11.84 % Favored : 86.05 % 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: 2.28 (0.38), residues: 530 helix: 2.81 (0.31), residues: 268 sheet: 0.44 (0.49), residues: 95 loop : 0.03 (0.54), residues: 167 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 0.009 0.001 PHE A 537 TYR 0.013 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 47 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.576 Fit side-chains REVERT: A 48 MET cc_start: 0.8716 (mpp) cc_final: 0.8091 (mpp) REVERT: A 102 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8761 (mp0) REVERT: A 202 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7296 (t80) REVERT: A 797 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6234 (ptp-170) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.1559 time to fit residues: 9.9809 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 : 0.621 ------------------------------------------------------------------------------- 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: 0.0570 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.073390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.058027 restraints weight = 15102.439| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.85 r_work: 0.2701 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0885 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= 0.346 Angle : 0.580 7.825 8110 Z= 0.305 Chirality : 0.039 0.206 925 Planarity : 0.004 0.031 835 Dihedral : 20.529 174.308 1433 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.81 % Allowed : 11.84 % Favored : 84.36 % 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: 2.10 (0.38), residues: 530 helix: 2.91 (0.31), residues: 261 sheet: 0.28 (0.48), residues: 102 loop : -0.34 (0.54), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 391 HIS 0.005 0.001 HIS A 609 PHE 0.013 0.002 PHE A 369 TYR 0.010 0.001 TYR A 22 ARG 0.002 0.000 ARG A 49 *********************** 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 : 0.570 Fit side-chains REVERT: A 48 MET cc_start: 0.8653 (mpp) cc_final: 0.7991 (mpp) REVERT: A 70 CYS cc_start: 0.9310 (t) cc_final: 0.8349 (p) REVERT: A 99 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9155 (tt) REVERT: A 102 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8702 (mp0) REVERT: A 202 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7263 (t80) REVERT: A 797 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6248 (ptm160) outliers start: 18 outliers final: 9 residues processed: 50 average time/residue: 0.1803 time to fit residues: 12.2464 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 : 0.577 ------------------------------------------------------------------------------- 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 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 797 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.075789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.060369 restraints weight = 15186.476| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.87 r_work: 0.2753 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1046 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= 0.180 Angle : 0.512 8.149 8110 Z= 0.269 Chirality : 0.036 0.156 925 Planarity : 0.003 0.034 835 Dihedral : 20.439 173.987 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.11 % Allowed : 13.11 % 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: 2.53 (0.38), residues: 530 helix: 3.15 (0.31), residues: 265 sheet: 0.28 (0.49), residues: 95 loop : 0.14 (0.54), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.002 0.001 HIS A 609 PHE 0.010 0.001 PHE A 390 TYR 0.009 0.001 TYR A 44 ARG 0.006 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 48 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 202 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7228 (t80) REVERT: A 714 ASN cc_start: 0.7230 (OUTLIER) cc_final: 0.6213 (p0) REVERT: A 797 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6245 (ptm160) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.1686 time to fit residues: 11.0296 Evaluate side-chains 45 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.075357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.059918 restraints weight = 14867.063| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.83 r_work: 0.2743 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1104 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= 0.216 Angle : 0.519 8.128 8110 Z= 0.272 Chirality : 0.036 0.164 925 Planarity : 0.003 0.038 835 Dihedral : 20.425 174.338 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.17 % Allowed : 13.32 % Favored : 83.51 % 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: 2.49 (0.38), residues: 530 helix: 3.15 (0.31), residues: 265 sheet: 0.26 (0.47), residues: 100 loop : 0.04 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 22 ARG 0.006 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 : 0.618 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8629 (mpp) cc_final: 0.7895 (mpp) REVERT: A 70 CYS cc_start: 0.9291 (t) cc_final: 0.8344 (p) REVERT: A 99 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9117 (tt) REVERT: A 202 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 714 ASN cc_start: 0.7227 (OUTLIER) cc_final: 0.6188 (p0) REVERT: A 797 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6197 (ptm160) outliers start: 15 outliers final: 9 residues processed: 50 average time/residue: 0.1724 time to fit residues: 12.0326 Evaluate side-chains 48 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 55 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3210 r_free = 0.3210 target = 0.073534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.058125 restraints weight = 15058.387| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.80 r_work: 0.2704 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1203 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= 0.332 Angle : 0.572 9.398 8110 Z= 0.298 Chirality : 0.039 0.202 925 Planarity : 0.004 0.034 835 Dihedral : 20.499 173.795 1433 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.38 % Allowed : 13.32 % 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: 2.25 (0.38), residues: 530 helix: 2.97 (0.31), residues: 267 sheet: 0.22 (0.48), residues: 100 loop : -0.21 (0.55), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 391 HIS 0.005 0.001 HIS A 609 PHE 0.011 0.001 PHE A 390 TYR 0.010 0.001 TYR A 22 ARG 0.006 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 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8602 (mpp) cc_final: 0.7877 (mpp) REVERT: A 70 CYS cc_start: 0.9293 (t) cc_final: 0.8373 (p) REVERT: A 99 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9150 (tt) REVERT: A 202 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7361 (t80) REVERT: A 714 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6265 (p0) REVERT: A 797 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6165 (ptp-170) outliers start: 16 outliers final: 11 residues processed: 51 average time/residue: 0.1806 time to fit residues: 12.4042 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 : 0.542 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.075485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.059904 restraints weight = 15025.679| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.91 r_work: 0.2747 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1257 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= 0.185 Angle : 0.516 8.499 8110 Z= 0.270 Chirality : 0.036 0.159 925 Planarity : 0.003 0.037 835 Dihedral : 20.444 173.648 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.59 % Allowed : 14.16 % Favored : 82.24 % 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: 2.56 (0.39), residues: 530 helix: 3.20 (0.31), residues: 265 sheet: 0.28 (0.48), residues: 100 loop : 0.12 (0.57), 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 22 ARG 0.007 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 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8605 (mpp) cc_final: 0.7897 (mpp) REVERT: A 70 CYS cc_start: 0.9319 (t) cc_final: 0.8403 (p) REVERT: A 99 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9127 (tt) REVERT: A 102 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8629 (mp0) REVERT: A 202 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7327 (t80) REVERT: A 714 ASN cc_start: 0.7243 (OUTLIER) cc_final: 0.6231 (p0) REVERT: A 797 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6204 (ptp-170) outliers start: 17 outliers final: 10 residues processed: 50 average time/residue: 0.1664 time to fit residues: 11.5232 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 : 0.533 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.075394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.059792 restraints weight = 15030.943| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.92 r_work: 0.2744 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1340 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= 0.207 Angle : 0.518 8.386 8110 Z= 0.270 Chirality : 0.036 0.164 925 Planarity : 0.004 0.039 835 Dihedral : 20.420 174.042 1433 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.38 % Allowed : 13.95 % 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: 2.59 (0.39), residues: 530 helix: 3.20 (0.31), residues: 265 sheet: 0.30 (0.48), residues: 100 loop : 0.16 (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 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8580 (mpp) cc_final: 0.7876 (mpp) REVERT: A 70 CYS cc_start: 0.9295 (t) cc_final: 0.8378 (p) REVERT: A 99 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9114 (tt) REVERT: A 102 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8633 (mp0) REVERT: A 202 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7327 (t80) REVERT: A 714 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6208 (p0) REVERT: A 797 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6183 (ptp-170) outliers start: 16 outliers final: 11 residues processed: 49 average time/residue: 0.1699 time to fit residues: 11.4683 Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 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 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 717 LEU 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: 0.9980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.074889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.059259 restraints weight = 15092.658| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.91 r_work: 0.2728 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1356 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= 0.247 Angle : 0.537 8.439 8110 Z= 0.280 Chirality : 0.037 0.178 925 Planarity : 0.004 0.037 835 Dihedral : 20.442 173.982 1433 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.59 % Allowed : 13.95 % 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: 2.34 (0.38), residues: 530 helix: 3.08 (0.31), residues: 267 sheet: 0.20 (0.49), residues: 100 loop : -0.18 (0.56), residues: 163 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 0.006 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 53 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8572 (mpp) cc_final: 0.7869 (mpp) REVERT: A 70 CYS cc_start: 0.9310 (t) cc_final: 0.8388 (p) REVERT: A 99 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9151 (tt) REVERT: A 102 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8663 (mp0) REVERT: A 202 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7353 (t80) REVERT: A 714 ASN cc_start: 0.7241 (OUTLIER) cc_final: 0.6152 (p0) REVERT: A 797 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6203 (ptp-170) outliers start: 17 outliers final: 11 residues processed: 51 average time/residue: 0.1633 time to fit residues: 11.5416 Evaluate side-chains 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 102 GLU 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 717 LEU 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: 0.8980 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.075249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.059686 restraints weight = 15133.426| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.91 r_work: 0.2741 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1425 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 : 0.526 8.499 8110 Z= 0.274 Chirality : 0.036 0.170 925 Planarity : 0.004 0.039 835 Dihedral : 20.439 173.869 1433 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.17 % Allowed : 14.38 % 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: 2.53 (0.39), residues: 530 helix: 3.21 (0.31), residues: 265 sheet: 0.18 (0.49), residues: 100 loop : 0.11 (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 0.007 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 51 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8571 (mpp) cc_final: 0.7865 (mpp) REVERT: A 70 CYS cc_start: 0.9293 (t) cc_final: 0.8376 (p) REVERT: A 99 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9107 (tt) REVERT: A 102 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8648 (mp0) REVERT: A 202 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7327 (t80) REVERT: A 714 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.6142 (p0) REVERT: A 726 LEU cc_start: 0.8562 (mm) cc_final: 0.8272 (mt) REVERT: A 797 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6304 (ptm160) outliers start: 15 outliers final: 10 residues processed: 49 average time/residue: 0.1674 time to fit residues: 11.4009 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 : 0.589 ------------------------------------------------------------------------------- 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 102 GLU 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 714 ASN Chi-restraints excluded: chain A residue 717 LEU 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: 5.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.0670 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.075618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.060007 restraints weight = 15111.474| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.92 r_work: 0.2747 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1432 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= 0.188 Angle : 0.515 8.524 8110 Z= 0.270 Chirality : 0.036 0.158 925 Planarity : 0.003 0.039 835 Dihedral : 20.427 173.927 1433 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.59 % Allowed : 13.95 % 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: 2.54 (0.39), residues: 530 helix: 3.21 (0.31), residues: 265 sheet: 0.18 (0.49), residues: 100 loop : 0.12 (0.57), 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 0.009 0.001 PHE A 390 TYR 0.009 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: 2598.43 seconds wall clock time: 45 minutes 29.58 seconds (2729.58 seconds total)