Starting phenix.real_space_refine on Tue Jan 14 12:51:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6j_38988/01_2025/8y6j_38988_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6j_38988/01_2025/8y6j_38988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y6j_38988/01_2025/8y6j_38988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6j_38988/01_2025/8y6j_38988.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6j_38988/01_2025/8y6j_38988_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6j_38988/01_2025/8y6j_38988_neut.cif" } resolution = 3.46 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= 0.002 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4368 2.51 5 N 1062 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 6650 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3325 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3325 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 4.43, per 1000 atoms: 0.67 Number of scatterers: 6650 At special positions: 0 Unit cell: (73.84, 107.12, 81.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1178 8.00 N 1062 7.00 C 4368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 518 " distance=2.03 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: 1.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 56 through 70 removed outlier: 3.506A pdb=" N LYS A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 94 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.723A pdb=" N LEU A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 220 through 245 Processing helix chain 'A' and resid 245 through 256 removed outlier: 4.133A pdb=" N ARG A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 289 through 302 Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.512A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.824A pdb=" N ALA A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 371 removed outlier: 3.856A pdb=" N TRP A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 380 through 396 removed outlier: 4.125A pdb=" N ARG A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 424 through 430 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 459 through 473 Processing helix chain 'A' and resid 473 through 480 Processing helix chain 'A' and resid 485 through 499 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 530 through 546 Processing helix chain 'B' and resid 57 through 70 removed outlier: 3.629A pdb=" N LYS B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 94 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.751A pdb=" N LEU B 128 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 144 Processing helix chain 'B' and resid 144 through 159 Processing helix chain 'B' and resid 220 through 245 Processing helix chain 'B' and resid 245 through 256 removed outlier: 4.106A pdb=" N ARG B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 272 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 289 through 302 Proline residue: B 298 - end of helix Processing helix chain 'B' and resid 306 through 323 removed outlier: 3.560A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.833A pdb=" N ALA B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 371 removed outlier: 3.870A pdb=" N TRP B 371 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 380 through 398 removed outlier: 4.116A pdb=" N ARG B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLN B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 409 through 422 Processing helix chain 'B' and resid 424 through 430 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 473 through 480 Processing helix chain 'B' and resid 485 through 499 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 530 through 546 467 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2020 1.34 - 1.46: 1496 1.46 - 1.58: 3210 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6792 Sorted by residual: bond pdb=" CA VAL A 456 " pdb=" CB VAL A 456 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.34e-02 5.57e+03 1.57e+00 bond pdb=" CA GLU B 548 " pdb=" CB GLU B 548 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.53e+00 bond pdb=" CA GLN B 332 " pdb=" CB GLN B 332 " ideal model delta sigma weight residual 1.532 1.551 -0.020 1.65e-02 3.67e+03 1.42e+00 bond pdb=" CA VAL B 456 " pdb=" CB VAL B 456 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.34e-02 5.57e+03 1.37e+00 bond pdb=" CB GLN A 332 " pdb=" CG GLN A 332 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 6787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 9093 1.92 - 3.84: 104 3.84 - 5.76: 14 5.76 - 7.69: 5 7.69 - 9.61: 2 Bond angle restraints: 9218 Sorted by residual: angle pdb=" CA GLU B 548 " pdb=" CB GLU B 548 " pdb=" CG GLU B 548 " ideal model delta sigma weight residual 114.10 123.71 -9.61 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA GLN B 332 " pdb=" CB GLN B 332 " pdb=" CG GLN B 332 " ideal model delta sigma weight residual 114.10 123.08 -8.98 2.00e+00 2.50e-01 2.02e+01 angle pdb=" N GLU B 548 " pdb=" CA GLU B 548 " pdb=" CB GLU B 548 " ideal model delta sigma weight residual 110.49 117.95 -7.46 1.69e+00 3.50e-01 1.95e+01 angle pdb=" C LYS B 547 " pdb=" N GLU B 548 " pdb=" CA GLU B 548 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" CA GLN A 332 " pdb=" CB GLN A 332 " pdb=" CG GLN A 332 " ideal model delta sigma weight residual 114.10 121.69 -7.59 2.00e+00 2.50e-01 1.44e+01 ... (remaining 9213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 3342 15.59 - 31.17: 497 31.17 - 46.76: 138 46.76 - 62.35: 32 62.35 - 77.93: 5 Dihedral angle restraints: 4014 sinusoidal: 1540 harmonic: 2474 Sorted by residual: dihedral pdb=" CA LYS B 547 " pdb=" C LYS B 547 " pdb=" N GLU B 548 " pdb=" CA GLU B 548 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLN B 397 " pdb=" C GLN B 397 " pdb=" N ALA B 398 " pdb=" CA ALA B 398 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLN A 397 " pdb=" C GLN A 397 " pdb=" N ALA A 398 " pdb=" CA ALA A 398 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 835 0.040 - 0.080: 233 0.080 - 0.120: 35 0.120 - 0.160: 2 0.160 - 0.200: 1 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA GLU B 548 " pdb=" N GLU B 548 " pdb=" C GLU B 548 " pdb=" CB GLU B 548 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA SER B 308 " pdb=" N SER B 308 " pdb=" C SER B 308 " pdb=" CB SER B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA SER A 308 " pdb=" N SER A 308 " pdb=" C SER A 308 " pdb=" CB SER A 308 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1103 not shown) Planarity restraints: 1120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 548 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" CD GLU B 548 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU B 548 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 548 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 547 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C LYS A 547 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS A 547 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A 548 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 99 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 100 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " -0.020 5.00e-02 4.00e+02 ... (remaining 1117 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 234 2.72 - 3.27: 7187 3.27 - 3.81: 11568 3.81 - 4.36: 12791 4.36 - 4.90: 22678 Nonbonded interactions: 54458 Sorted by model distance: nonbonded pdb=" OH TYR B 79 " pdb=" O MET B 142 " model vdw 2.181 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG SER A 119 " model vdw 2.191 3.040 nonbonded pdb=" OH TYR A 79 " pdb=" O MET A 142 " model vdw 2.222 3.040 nonbonded pdb=" OE2 GLU B 370 " pdb=" OG SER B 409 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU A 370 " pdb=" OG SER A 409 " model vdw 2.234 3.040 ... (remaining 54453 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.240 Find NCS groups from input model: 0.190 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.003 0.035 6792 Z= 0.192 Angle : 0.549 9.607 9218 Z= 0.293 Chirality : 0.036 0.200 1106 Planarity : 0.003 0.035 1120 Dihedral : 16.136 77.931 2404 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 23.47 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.30), residues: 838 helix: 2.62 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.23 (0.47), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 134 HIS 0.009 0.002 HIS A 333 PHE 0.013 0.001 PHE B 390 TYR 0.017 0.002 TYR B 79 ARG 0.001 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.780 Fit side-chains REVERT: A 93 ASN cc_start: 0.7604 (m110) cc_final: 0.7110 (m110) REVERT: A 548 GLU cc_start: 0.7800 (mp0) cc_final: 0.7525 (mp0) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1579 time to fit residues: 21.9319 Evaluate side-chains 92 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.148372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.118828 restraints weight = 7509.369| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.90 r_work: 0.3131 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6792 Z= 0.203 Angle : 0.497 7.184 9218 Z= 0.265 Chirality : 0.036 0.117 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.666 19.717 896 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.93 % Allowed : 21.87 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.15 (0.30), residues: 838 helix: 2.71 (0.20), residues: 614 sheet: None (None), residues: 0 loop : 0.32 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 134 HIS 0.005 0.002 HIS B 333 PHE 0.013 0.001 PHE B 227 TYR 0.019 0.002 TYR A 79 ARG 0.003 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.637 Fit side-chains REVERT: A 93 ASN cc_start: 0.7605 (m110) cc_final: 0.7011 (m110) REVERT: A 133 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7159 (mp) REVERT: B 133 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7124 (mp) REVERT: B 414 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7882 (tp) REVERT: B 548 GLU cc_start: 0.8092 (pm20) cc_final: 0.7852 (pm20) outliers start: 22 outliers final: 7 residues processed: 111 average time/residue: 0.1436 time to fit residues: 23.1530 Evaluate side-chains 103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.146396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116993 restraints weight = 7587.041| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.88 r_work: 0.3102 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6792 Z= 0.232 Angle : 0.502 5.907 9218 Z= 0.266 Chirality : 0.036 0.116 1106 Planarity : 0.003 0.033 1120 Dihedral : 3.726 20.715 896 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.67 % Allowed : 23.20 % Favored : 74.13 % 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: 3.06 (0.30), residues: 838 helix: 2.63 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.28 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 134 HIS 0.005 0.001 HIS A 333 PHE 0.014 0.001 PHE B 227 TYR 0.018 0.002 TYR A 79 ARG 0.001 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.731 Fit side-chains REVERT: A 93 ASN cc_start: 0.7629 (m110) cc_final: 0.7050 (m110) REVERT: A 133 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7224 (mp) REVERT: B 133 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7179 (mp) REVERT: B 414 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7898 (tp) REVERT: B 548 GLU cc_start: 0.8227 (pm20) cc_final: 0.7866 (pm20) outliers start: 20 outliers final: 11 residues processed: 108 average time/residue: 0.1341 time to fit residues: 21.4030 Evaluate side-chains 107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.147044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117631 restraints weight = 7722.233| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.89 r_work: 0.3111 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6792 Z= 0.205 Angle : 0.491 5.987 9218 Z= 0.260 Chirality : 0.036 0.119 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.713 20.431 896 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.67 % Allowed : 22.93 % Favored : 74.40 % 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: 3.11 (0.30), residues: 838 helix: 2.68 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.24 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 134 HIS 0.006 0.001 HIS A 333 PHE 0.013 0.001 PHE B 227 TYR 0.017 0.002 TYR A 79 ARG 0.001 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.757 Fit side-chains REVERT: A 93 ASN cc_start: 0.7656 (m110) cc_final: 0.7073 (m110) REVERT: A 133 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7226 (mp) REVERT: B 133 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7167 (mp) REVERT: B 310 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8109 (mm) REVERT: B 414 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7889 (tp) outliers start: 20 outliers final: 11 residues processed: 110 average time/residue: 0.1443 time to fit residues: 23.0442 Evaluate side-chains 107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 0.0050 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 6 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.149481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120356 restraints weight = 7593.940| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.86 r_work: 0.3141 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6792 Z= 0.164 Angle : 0.481 6.488 9218 Z= 0.254 Chirality : 0.035 0.118 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.632 19.761 896 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.07 % Allowed : 23.07 % Favored : 73.87 % 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: 3.22 (0.30), residues: 838 helix: 2.76 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.27 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 134 HIS 0.004 0.001 HIS A 333 PHE 0.016 0.001 PHE A 390 TYR 0.016 0.001 TYR A 79 ARG 0.001 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.705 Fit side-chains REVERT: A 93 ASN cc_start: 0.7657 (m110) cc_final: 0.6983 (m110) REVERT: A 133 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7119 (mp) REVERT: A 310 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8088 (mm) REVERT: A 348 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8843 (m) REVERT: B 133 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7157 (mp) REVERT: B 414 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7851 (tp) outliers start: 23 outliers final: 13 residues processed: 113 average time/residue: 0.1334 time to fit residues: 22.3747 Evaluate side-chains 109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 64 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.149582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.120424 restraints weight = 7497.114| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.87 r_work: 0.3146 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6792 Z= 0.170 Angle : 0.481 6.958 9218 Z= 0.253 Chirality : 0.036 0.129 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.638 19.850 896 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.60 % Allowed : 22.13 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.30), residues: 838 helix: 2.82 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.31 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 134 HIS 0.004 0.001 HIS A 333 PHE 0.020 0.001 PHE A 390 TYR 0.016 0.001 TYR A 79 ARG 0.001 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.747 Fit side-chains REVERT: A 93 ASN cc_start: 0.7628 (m110) cc_final: 0.6917 (m110) REVERT: A 133 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7100 (mp) REVERT: A 310 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 333 HIS cc_start: 0.7995 (m90) cc_final: 0.7745 (m90) REVERT: A 348 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8811 (m) REVERT: A 548 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: B 133 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7168 (mp) REVERT: B 310 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 348 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8801 (m) REVERT: B 414 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7882 (tp) outliers start: 27 outliers final: 15 residues processed: 112 average time/residue: 0.1492 time to fit residues: 24.6472 Evaluate side-chains 114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 154 TYR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 0.0770 chunk 77 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.148563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.120307 restraints weight = 7525.061| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.77 r_work: 0.3148 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6792 Z= 0.188 Angle : 0.489 7.360 9218 Z= 0.256 Chirality : 0.036 0.127 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.618 20.201 896 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.20 % Allowed : 23.33 % Favored : 73.47 % 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: 3.35 (0.30), residues: 838 helix: 2.85 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.33 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 134 HIS 0.004 0.001 HIS A 333 PHE 0.019 0.001 PHE A 390 TYR 0.016 0.001 TYR A 79 ARG 0.001 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.732 Fit side-chains REVERT: A 93 ASN cc_start: 0.7615 (m110) cc_final: 0.6916 (m110) REVERT: A 133 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7167 (mp) REVERT: A 310 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8119 (mm) REVERT: A 333 HIS cc_start: 0.8076 (m90) cc_final: 0.7739 (m90) REVERT: A 348 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8865 (m) REVERT: A 548 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: B 133 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7187 (mp) REVERT: B 310 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8144 (mm) REVERT: B 348 SER cc_start: 0.9183 (OUTLIER) cc_final: 0.8834 (m) REVERT: B 414 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7893 (tp) REVERT: B 548 GLU cc_start: 0.8104 (pm20) cc_final: 0.7668 (pm20) outliers start: 24 outliers final: 14 residues processed: 109 average time/residue: 0.1388 time to fit residues: 22.4100 Evaluate side-chains 113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 154 TYR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 0.0170 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.149385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120050 restraints weight = 7554.028| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.89 r_work: 0.3142 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6792 Z= 0.174 Angle : 0.487 7.790 9218 Z= 0.255 Chirality : 0.036 0.127 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.599 20.065 896 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.33 % Allowed : 22.93 % Favored : 73.73 % 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: 3.44 (0.30), residues: 838 helix: 2.92 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.38 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 134 HIS 0.003 0.001 HIS A 333 PHE 0.018 0.001 PHE A 390 TYR 0.016 0.001 TYR A 79 ARG 0.001 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.747 Fit side-chains REVERT: A 93 ASN cc_start: 0.7580 (m110) cc_final: 0.6840 (m110) REVERT: A 133 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7133 (mp) REVERT: A 310 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8050 (mm) REVERT: A 333 HIS cc_start: 0.8158 (m90) cc_final: 0.7777 (m90) REVERT: A 348 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8830 (m) REVERT: A 548 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: B 133 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7104 (mp) REVERT: B 310 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8110 (mm) REVERT: B 348 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8803 (m) REVERT: B 414 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7837 (tp) outliers start: 25 outliers final: 15 residues processed: 112 average time/residue: 0.1507 time to fit residues: 24.8885 Evaluate side-chains 116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 154 TYR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 0.0470 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 0.0010 chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.149497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120575 restraints weight = 7563.435| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.87 r_work: 0.3150 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6792 Z= 0.167 Angle : 0.491 8.119 9218 Z= 0.255 Chirality : 0.036 0.131 1106 Planarity : 0.003 0.029 1120 Dihedral : 3.571 19.990 896 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.93 % Allowed : 23.33 % Favored : 73.73 % 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: 3.51 (0.30), residues: 838 helix: 2.97 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.42 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 134 HIS 0.004 0.001 HIS A 333 PHE 0.018 0.001 PHE A 390 TYR 0.016 0.001 TYR B 79 ARG 0.001 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.757 Fit side-chains REVERT: A 93 ASN cc_start: 0.7583 (m110) cc_final: 0.6841 (m110) REVERT: A 133 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7194 (mp) REVERT: A 310 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 333 HIS cc_start: 0.8197 (m90) cc_final: 0.7895 (m-70) REVERT: A 548 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: B 133 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7178 (mp) REVERT: B 310 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8154 (mm) REVERT: B 348 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8853 (m) REVERT: B 414 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7913 (tp) REVERT: B 548 GLU cc_start: 0.8150 (pm20) cc_final: 0.7767 (pm20) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 0.1427 time to fit residues: 23.3733 Evaluate side-chains 116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 154 TYR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.147772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118345 restraints weight = 7626.732| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.90 r_work: 0.3124 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6792 Z= 0.210 Angle : 0.503 8.201 9218 Z= 0.261 Chirality : 0.036 0.127 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.620 20.637 896 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.07 % Allowed : 23.07 % Favored : 73.87 % 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: 3.46 (0.30), residues: 838 helix: 2.93 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.41 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 134 HIS 0.008 0.001 HIS A 333 PHE 0.017 0.001 PHE A 390 TYR 0.017 0.002 TYR A 79 ARG 0.002 0.000 ARG A 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.754 Fit side-chains REVERT: A 93 ASN cc_start: 0.7586 (m110) cc_final: 0.6843 (m110) REVERT: A 310 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 348 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8834 (m) REVERT: A 548 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: B 133 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7134 (mp) REVERT: B 310 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8185 (mm) REVERT: B 348 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8809 (m) REVERT: B 414 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7880 (tp) REVERT: B 548 GLU cc_start: 0.8170 (pm20) cc_final: 0.7719 (pm20) outliers start: 23 outliers final: 14 residues processed: 111 average time/residue: 0.1353 time to fit residues: 22.1163 Evaluate side-chains 112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 154 TYR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 57 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.148390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.120046 restraints weight = 7626.086| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.80 r_work: 0.3134 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6792 Z= 0.186 Angle : 0.497 8.298 9218 Z= 0.259 Chirality : 0.036 0.129 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.603 20.382 896 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.93 % Allowed : 23.33 % Favored : 73.73 % 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: 3.49 (0.30), residues: 838 helix: 2.95 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.40 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 134 HIS 0.006 0.001 HIS A 333 PHE 0.017 0.001 PHE A 390 TYR 0.016 0.002 TYR A 79 ARG 0.002 0.000 ARG A 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3220.02 seconds wall clock time: 60 minutes 1.13 seconds (3601.13 seconds total)