Starting phenix.real_space_refine on Tue Mar 11 20:42:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6j_38988/03_2025/8y6j_38988_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6j_38988/03_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_38988/03_2025/8y6j_38988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6j_38988/03_2025/8y6j_38988.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6j_38988/03_2025/8y6j_38988_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6j_38988/03_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.79, per 1000 atoms: 0.72 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: 1.73 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: 0.61 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: 1.92 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 0.740 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.720 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- 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 : 0.722 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: 0.1492 time to fit residues: 20.7250 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 : 0.730 ------------------------------------------------------------------------------- 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: 0.4980 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.148493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119023 restraints weight = 7508.448| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.89 r_work: 0.3132 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0564 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= 0.196 Angle : 0.493 6.957 9218 Z= 0.263 Chirality : 0.036 0.118 1106 Planarity : 0.003 0.031 1120 Dihedral : 3.659 19.682 896 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.93 % Allowed : 21.73 % Favored : 75.33 % 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: 3.14 (0.30), residues: 838 helix: 2.67 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.37 (0.49), residues: 220 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 0.002 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 119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.692 Fit side-chains REVERT: A 93 ASN cc_start: 0.7628 (m110) cc_final: 0.7036 (m110) REVERT: A 133 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7231 (mp) REVERT: B 133 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7200 (mp) REVERT: B 414 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7926 (tp) REVERT: B 548 GLU cc_start: 0.8135 (pm20) cc_final: 0.7897 (pm20) outliers start: 22 outliers final: 6 residues processed: 112 average time/residue: 0.1462 time to fit residues: 23.7319 Evaluate side-chains 103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 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: 0.9990 chunk 26 optimal weight: 0.9980 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 = 0.3589 r_free = 0.3589 target = 0.147612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118272 restraints weight = 7551.685| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.87 r_work: 0.3118 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0795 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= 0.205 Angle : 0.492 6.038 9218 Z= 0.261 Chirality : 0.036 0.121 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.662 20.341 896 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.27 % Allowed : 23.60 % 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: 3.12 (0.30), residues: 838 helix: 2.68 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.30 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 134 HIS 0.005 0.001 HIS A 333 PHE 0.013 0.001 PHE B 227 TYR 0.017 0.002 TYR A 79 ARG 0.002 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 112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.706 Fit side-chains REVERT: A 93 ASN cc_start: 0.7637 (m110) cc_final: 0.7023 (m110) REVERT: A 133 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7196 (mp) REVERT: B 133 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7199 (mp) REVERT: B 414 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7894 (tp) outliers start: 17 outliers final: 8 residues processed: 107 average time/residue: 0.1349 time to fit residues: 21.2987 Evaluate side-chains 103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.146884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.117329 restraints weight = 7730.409| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.89 r_work: 0.3110 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.0902 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= 0.219 Angle : 0.494 6.238 9218 Z= 0.261 Chirality : 0.036 0.118 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.690 20.493 896 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.80 % Allowed : 22.93 % 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: 3.11 (0.30), residues: 838 helix: 2.67 (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 0.007 0.001 TRP A 134 HIS 0.007 0.001 HIS A 333 PHE 0.015 0.001 PHE A 390 TYR 0.017 0.002 TYR A 79 ARG 0.001 0.000 ARG A 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 113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.654 Fit side-chains REVERT: A 93 ASN cc_start: 0.7691 (m110) cc_final: 0.7074 (m110) REVERT: A 133 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7289 (mp) REVERT: B 133 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7284 (mp) REVERT: B 414 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7947 (tp) outliers start: 21 outliers final: 10 residues processed: 108 average time/residue: 0.1436 time to fit residues: 22.3972 Evaluate side-chains 105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.143826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.114594 restraints weight = 7678.909| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.82 r_work: 0.3082 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6792 Z= 0.289 Angle : 0.528 6.708 9218 Z= 0.278 Chirality : 0.037 0.124 1106 Planarity : 0.003 0.034 1120 Dihedral : 3.821 21.846 896 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.73 % Allowed : 22.93 % Favored : 73.33 % 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: 2.95 (0.30), residues: 838 helix: 2.55 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.25 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 134 HIS 0.004 0.001 HIS A 333 PHE 0.017 0.002 PHE A 390 TYR 0.016 0.002 TYR A 79 ARG 0.002 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: 28 poor density : 89 time to evaluate : 0.674 Fit side-chains REVERT: A 107 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7499 (mp) REVERT: A 133 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7421 (mp) REVERT: A 310 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8169 (mm) REVERT: A 333 HIS cc_start: 0.8175 (m90) cc_final: 0.7900 (m90) REVERT: A 548 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: B 133 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7373 (mp) REVERT: B 310 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8182 (mm) REVERT: B 348 SER cc_start: 0.9268 (OUTLIER) cc_final: 0.8889 (m) outliers start: 28 outliers final: 18 residues processed: 111 average time/residue: 0.1332 time to fit residues: 21.7411 Evaluate side-chains 115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 107 LEU 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 518 CYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 113 SER 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 473 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.145982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.116699 restraints weight = 7547.262| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.88 r_work: 0.3097 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6792 Z= 0.214 Angle : 0.502 6.883 9218 Z= 0.264 Chirality : 0.036 0.126 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.765 21.369 896 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.07 % Allowed : 23.60 % Favored : 73.33 % 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: 3.07 (0.30), residues: 838 helix: 2.64 (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 0.008 0.001 TRP A 134 HIS 0.003 0.001 HIS A 333 PHE 0.017 0.001 PHE A 390 TYR 0.016 0.002 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 114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.686 Fit side-chains REVERT: A 133 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7216 (mp) REVERT: A 310 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8030 (mm) REVERT: A 333 HIS cc_start: 0.8204 (m90) cc_final: 0.7977 (m-70) REVERT: A 348 SER cc_start: 0.9168 (OUTLIER) cc_final: 0.8800 (m) REVERT: B 133 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7177 (mp) REVERT: B 310 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 414 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7756 (tp) outliers start: 23 outliers final: 13 residues processed: 110 average time/residue: 0.1331 time to fit residues: 21.7704 Evaluate side-chains 109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.145916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116618 restraints weight = 7557.862| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.87 r_work: 0.3100 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6792 Z= 0.215 Angle : 0.503 7.160 9218 Z= 0.264 Chirality : 0.036 0.131 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.723 21.278 896 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.87 % Allowed : 23.20 % Favored : 72.93 % 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: 3.12 (0.30), residues: 838 helix: 2.67 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.30 (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 0.017 0.001 PHE A 390 TYR 0.016 0.002 TYR A 79 ARG 0.002 0.000 ARG A 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 122 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.762 Fit side-chains REVERT: A 133 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7206 (mp) REVERT: A 310 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 333 HIS cc_start: 0.8328 (m90) cc_final: 0.7941 (m90) REVERT: A 348 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8808 (m) REVERT: A 548 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: B 133 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7191 (mp) REVERT: B 310 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8115 (mm) REVERT: B 344 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7656 (t) REVERT: B 348 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8787 (m) REVERT: B 414 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7763 (tp) outliers start: 29 outliers final: 17 residues processed: 115 average time/residue: 0.1349 time to fit residues: 23.0488 Evaluate side-chains 116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 220 VAL 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 113 SER 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 305 THR 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 344 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 512 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: 1.9990 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.0270 chunk 62 optimal weight: 0.0470 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 0.0000 overall best weight: 0.1940 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.150458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122570 restraints weight = 7560.629| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.78 r_work: 0.3180 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6792 Z= 0.147 Angle : 0.491 7.944 9218 Z= 0.259 Chirality : 0.036 0.132 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.642 20.027 896 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.47 % Allowed : 23.47 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.30), residues: 838 helix: 2.86 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.34 (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 0.018 0.001 PHE A 390 TYR 0.015 0.002 TYR B 79 ARG 0.001 0.000 ARG A 287 *********************** 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: 26 poor density : 93 time to evaluate : 0.719 Fit side-chains REVERT: A 93 ASN cc_start: 0.7631 (m110) cc_final: 0.6927 (m110) REVERT: A 133 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7115 (mp) REVERT: A 310 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8086 (mm) REVERT: A 548 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: B 133 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7106 (mp) REVERT: B 310 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8120 (mm) REVERT: B 344 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7581 (t) REVERT: B 348 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8823 (m) REVERT: B 414 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7717 (tp) REVERT: B 548 GLU cc_start: 0.8192 (pm20) cc_final: 0.7762 (pm20) outliers start: 26 outliers final: 14 residues processed: 113 average time/residue: 0.1303 time to fit residues: 21.9775 Evaluate side-chains 112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 220 VAL 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 305 THR 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 344 VAL 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: 0.7980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 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 = 0.3570 r_free = 0.3570 target = 0.145823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.117120 restraints weight = 7631.293| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.81 r_work: 0.3109 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.004 0.038 6792 Z= 0.249 Angle : 0.531 10.130 9218 Z= 0.274 Chirality : 0.037 0.129 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.727 21.257 896 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.20 % Allowed : 23.60 % Favored : 73.20 % 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: 3.30 (0.30), residues: 838 helix: 2.80 (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 A 134 HIS 0.005 0.001 HIS A 333 PHE 0.016 0.002 PHE A 390 TYR 0.024 0.002 TYR A 339 ARG 0.003 0.000 ARG A 221 *********************** 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 118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.758 Fit side-chains REVERT: A 93 ASN cc_start: 0.7639 (m110) cc_final: 0.6973 (m110) REVERT: A 133 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7248 (mp) REVERT: A 310 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8105 (mm) REVERT: A 333 HIS cc_start: 0.8247 (m90) cc_final: 0.7750 (m90) REVERT: A 339 TYR cc_start: 0.7803 (t80) cc_final: 0.7326 (t80) REVERT: A 548 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: B 310 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8126 (mm) REVERT: B 344 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7658 (t) REVERT: B 348 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8829 (m) REVERT: B 414 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7755 (tp) outliers start: 24 outliers final: 14 residues processed: 113 average time/residue: 0.1357 time to fit residues: 22.6548 Evaluate side-chains 114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 TYR 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 154 TYR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 305 THR 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 344 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 361 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.147691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119342 restraints weight = 7648.883| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.81 r_work: 0.3136 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6792 Z= 0.184 Angle : 0.504 8.410 9218 Z= 0.263 Chirality : 0.036 0.135 1106 Planarity : 0.003 0.031 1120 Dihedral : 3.686 20.785 896 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.20 % Allowed : 23.47 % Favored : 73.33 % 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: 3.40 (0.30), residues: 838 helix: 2.87 (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 0.009 0.001 TRP B 134 HIS 0.004 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 ********************** 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 116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.675 Fit side-chains REVERT: A 93 ASN cc_start: 0.7650 (m110) cc_final: 0.6941 (m110) REVERT: A 133 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7153 (mp) REVERT: A 310 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8072 (mm) REVERT: A 548 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: B 310 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8086 (mm) REVERT: B 344 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7628 (t) REVERT: B 348 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8824 (m) REVERT: B 414 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7796 (tp) REVERT: B 548 GLU cc_start: 0.8280 (pm20) cc_final: 0.7864 (pm20) outliers start: 24 outliers final: 15 residues processed: 110 average time/residue: 0.1292 time to fit residues: 21.1263 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 : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 TYR 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 154 TYR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 305 THR 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 344 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 512 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: 0.8980 chunk 40 optimal weight: 0.0060 chunk 57 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 73 optimal weight: 0.0030 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 overall best weight: 0.4206 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.148701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.119741 restraints weight = 7650.340| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.89 r_work: 0.3139 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1304 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= 0.171 Angle : 0.494 8.351 9218 Z= 0.258 Chirality : 0.036 0.130 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.623 20.228 896 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.07 % Allowed : 23.73 % Favored : 73.20 % 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: 3.47 (0.30), residues: 838 helix: 2.92 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.47 (0.50), 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 0.017 0.001 PHE A 390 TYR 0.015 0.001 TYR A 79 ARG 0.001 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.38 seconds wall clock time: 56 minutes 8.84 seconds (3368.84 seconds total)