Starting phenix.real_space_refine on Sat May 10 17:38:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6j_38988/05_2025/8y6j_38988_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6j_38988/05_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_38988/05_2025/8y6j_38988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6j_38988/05_2025/8y6j_38988.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6j_38988/05_2025/8y6j_38988_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6j_38988/05_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-5687/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: 3.80, per 1000 atoms: 0.57 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: 1.35 Conformation dependent library (CDL) restraints added in 774.5 milliseconds 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: 0.53 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: 1.60 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: 1.050 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.670 Find NCS groups from input model: 0.170 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:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- 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 6794 Z= 0.129 Angle : 0.549 9.607 9222 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 Details of bonding type rmsd hydrogen bonds : bond 0.10107 ( 467) hydrogen bonds : angle 4.52647 ( 1329) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.46700 ( 4) covalent geometry : bond 0.00297 ( 6792) covalent geometry : angle 0.54867 ( 9218) *********************** 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 : 0.785 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: 0.1509 time to fit residues: 21.0145 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 : 0.740 ------------------------------------------------------------------------------- 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 6794 Z= 0.133 Angle : 0.498 7.184 9222 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 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 467) hydrogen bonds : angle 3.82979 ( 1329) SS BOND : bond 0.00200 ( 2) SS BOND : angle 1.46464 ( 4) covalent geometry : bond 0.00313 ( 6792) covalent geometry : angle 0.49670 ( 9218) *********************** 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 : 0.724 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: 0.1417 time to fit residues: 22.8714 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 : 0.699 ------------------------------------------------------------------------------- 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: 0.0970 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 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: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.147034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117654 restraints weight = 7566.370| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.88 r_work: 0.3108 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6794 Z= 0.137 Angle : 0.495 5.984 9222 Z= 0.262 Chirality : 0.036 0.119 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.701 20.507 896 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.53 % Allowed : 23.20 % 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: 3.10 (0.30), residues: 838 helix: 2.67 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.29 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 134 HIS 0.003 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 A 312 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 467) hydrogen bonds : angle 3.69072 ( 1329) SS BOND : bond 0.00309 ( 2) SS BOND : angle 1.52265 ( 4) covalent geometry : bond 0.00329 ( 6792) covalent geometry : angle 0.49377 ( 9218) *********************** 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 113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.574 Fit side-chains REVERT: A 93 ASN cc_start: 0.7629 (m110) cc_final: 0.7047 (m-40) REVERT: A 133 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7201 (mp) REVERT: B 133 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7189 (mp) REVERT: B 414 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7885 (tp) outliers start: 19 outliers final: 10 residues processed: 107 average time/residue: 0.1310 time to fit residues: 20.7138 Evaluate side-chains 106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 52 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.147053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117568 restraints weight = 7718.473| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.90 r_work: 0.3109 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6794 Z= 0.137 Angle : 0.498 6.069 9222 Z= 0.263 Chirality : 0.036 0.122 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.708 20.471 896 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.07 % Allowed : 22.53 % 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 : 0.25 (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 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 467) hydrogen bonds : angle 3.64059 ( 1329) SS BOND : bond 0.00294 ( 2) SS BOND : angle 1.45371 ( 4) covalent geometry : bond 0.00330 ( 6792) covalent geometry : angle 0.49715 ( 9218) *********************** 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 117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.692 Fit side-chains REVERT: A 93 ASN cc_start: 0.7645 (m110) cc_final: 0.7024 (m110) REVERT: A 133 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7238 (mp) REVERT: B 133 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7217 (mp) REVERT: B 310 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8125 (mm) REVERT: B 414 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7905 (tp) outliers start: 23 outliers final: 11 residues processed: 111 average time/residue: 0.1454 time to fit residues: 23.3805 Evaluate side-chains 106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 310 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.144687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.115797 restraints weight = 7678.772| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.81 r_work: 0.3095 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6794 Z= 0.168 Angle : 0.518 6.379 9222 Z= 0.273 Chirality : 0.037 0.126 1106 Planarity : 0.003 0.033 1120 Dihedral : 3.795 21.171 896 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.87 % Allowed : 22.67 % 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: 2.99 (0.30), residues: 838 helix: 2.58 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.23 (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 0.015 0.002 PHE A 390 TYR 0.016 0.002 TYR A 79 ARG 0.002 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 467) hydrogen bonds : angle 3.67754 ( 1329) SS BOND : bond 0.00383 ( 2) SS BOND : angle 1.71722 ( 4) covalent geometry : bond 0.00412 ( 6792) covalent geometry : angle 0.51664 ( 9218) *********************** 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 121 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.732 Fit side-chains REVERT: A 107 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7468 (mp) REVERT: A 133 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7392 (mp) REVERT: A 310 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8086 (mm) REVERT: B 133 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7366 (mp) REVERT: B 310 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8177 (mm) REVERT: B 348 SER cc_start: 0.9250 (OUTLIER) cc_final: 0.8882 (m) REVERT: B 414 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7976 (tp) outliers start: 29 outliers final: 19 residues processed: 114 average time/residue: 0.1325 time to fit residues: 22.3507 Evaluate side-chains 117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 364 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 530 THR 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 414 LEU 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: 1.9990 chunk 68 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.145075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.115893 restraints weight = 7575.525| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.87 r_work: 0.3090 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6794 Z= 0.152 Angle : 0.512 6.759 9222 Z= 0.269 Chirality : 0.037 0.131 1106 Planarity : 0.003 0.033 1120 Dihedral : 3.787 21.226 896 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: 3.00 (0.30), residues: 838 helix: 2.60 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.22 (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 0.019 0.002 PHE A 390 TYR 0.016 0.002 TYR A 79 ARG 0.002 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 467) hydrogen bonds : angle 3.64109 ( 1329) SS BOND : bond 0.00331 ( 2) SS BOND : angle 1.62501 ( 4) covalent geometry : bond 0.00374 ( 6792) covalent geometry : angle 0.51117 ( 9218) *********************** 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 124 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.742 Fit side-chains REVERT: A 133 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7216 (mp) REVERT: A 310 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8049 (mm) REVERT: A 332 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8702 (tm-30) REVERT: A 348 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8796 (m) REVERT: A 548 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: B 133 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7203 (mp) REVERT: B 310 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8108 (mm) REVERT: B 348 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8801 (m) REVERT: B 414 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7880 (tp) outliers start: 28 outliers final: 18 residues processed: 117 average time/residue: 0.1290 time to fit residues: 22.2641 Evaluate side-chains 120 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 512 LEU Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 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 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.145773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116413 restraints weight = 7558.902| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.88 r_work: 0.3099 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6794 Z= 0.139 Angle : 0.506 7.200 9222 Z= 0.266 Chirality : 0.036 0.129 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.751 21.406 896 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.13 % Allowed : 22.80 % 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: 3.07 (0.30), residues: 838 helix: 2.64 (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 A 134 HIS 0.003 0.001 HIS A 333 PHE 0.018 0.002 PHE A 390 TYR 0.016 0.002 TYR A 79 ARG 0.001 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 467) hydrogen bonds : angle 3.60497 ( 1329) SS BOND : bond 0.00315 ( 2) SS BOND : angle 1.56095 ( 4) covalent geometry : bond 0.00339 ( 6792) covalent geometry : angle 0.50502 ( 9218) *********************** 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 124 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.730 Fit side-chains REVERT: A 133 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7207 (mp) REVERT: A 310 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8027 (mm) REVERT: A 332 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8651 (tm-30) REVERT: A 348 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8803 (m) REVERT: A 353 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8088 (mp) REVERT: A 548 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 133 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7173 (mp) REVERT: B 310 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8105 (mm) REVERT: B 348 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8800 (m) REVERT: B 414 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7868 (tp) outliers start: 31 outliers final: 19 residues processed: 114 average time/residue: 0.1296 time to fit residues: 21.8951 Evaluate side-chains 119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 353 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 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 348 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.146908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.117557 restraints weight = 7604.754| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.91 r_work: 0.3111 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6794 Z= 0.124 Angle : 0.499 7.593 9222 Z= 0.262 Chirality : 0.036 0.128 1106 Planarity : 0.003 0.031 1120 Dihedral : 3.720 21.012 896 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.60 % Allowed : 23.33 % 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: 3.20 (0.30), residues: 838 helix: 2.73 (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 0.007 0.001 TRP A 134 HIS 0.003 0.001 HIS B 333 PHE 0.018 0.001 PHE A 390 TYR 0.016 0.002 TYR A 79 ARG 0.001 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 467) hydrogen bonds : angle 3.55476 ( 1329) SS BOND : bond 0.00278 ( 2) SS BOND : angle 1.43918 ( 4) covalent geometry : bond 0.00299 ( 6792) covalent geometry : angle 0.49800 ( 9218) *********************** 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 123 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.775 Fit side-chains REVERT: A 93 ASN cc_start: 0.7640 (m110) cc_final: 0.7044 (m110) REVERT: A 310 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8039 (mm) REVERT: A 332 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8699 (tm-30) REVERT: A 348 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8810 (m) REVERT: A 353 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8092 (mp) REVERT: A 548 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: B 133 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7159 (mp) REVERT: B 414 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7847 (tp) REVERT: B 548 GLU cc_start: 0.8222 (pm20) cc_final: 0.7767 (pm20) outliers start: 27 outliers final: 18 residues processed: 115 average time/residue: 0.1357 time to fit residues: 23.1070 Evaluate side-chains 117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 113 SER 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 353 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.146515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117249 restraints weight = 7603.705| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.88 r_work: 0.3107 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6794 Z= 0.138 Angle : 0.520 9.524 9222 Z= 0.269 Chirality : 0.037 0.140 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.751 21.195 896 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.87 % Allowed : 23.07 % 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: 3.21 (0.30), residues: 838 helix: 2.73 (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 0.008 0.001 TRP A 134 HIS 0.006 0.001 HIS A 333 PHE 0.017 0.001 PHE A 390 TYR 0.021 0.002 TYR A 339 ARG 0.003 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 467) hydrogen bonds : angle 3.56721 ( 1329) SS BOND : bond 0.00317 ( 2) SS BOND : angle 1.51875 ( 4) covalent geometry : bond 0.00337 ( 6792) covalent geometry : angle 0.51869 ( 9218) *********************** 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 123 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.777 Fit side-chains REVERT: A 93 ASN cc_start: 0.7645 (m110) cc_final: 0.7013 (m110) REVERT: A 310 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 332 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 339 TYR cc_start: 0.7862 (t80) cc_final: 0.7359 (t80) REVERT: A 348 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8824 (m) REVERT: A 353 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8103 (mp) REVERT: A 548 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: B 133 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7208 (mp) REVERT: B 310 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8106 (mm) REVERT: B 348 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8805 (m) REVERT: B 414 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7864 (tp) REVERT: B 548 GLU cc_start: 0.8310 (pm20) cc_final: 0.7814 (pm20) outliers start: 29 outliers final: 19 residues processed: 115 average time/residue: 0.1330 time to fit residues: 22.5965 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 : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 113 SER 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 353 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 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 348 SER 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 8 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.147630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118352 restraints weight = 7643.607| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.89 r_work: 0.3122 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6794 Z= 0.119 Angle : 0.496 8.224 9222 Z= 0.260 Chirality : 0.036 0.130 1106 Planarity : 0.003 0.031 1120 Dihedral : 3.711 20.787 896 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.60 % Allowed : 23.20 % 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: 3.31 (0.30), residues: 838 helix: 2.82 (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 0.008 0.001 TRP A 134 HIS 0.006 0.001 HIS A 333 PHE 0.018 0.001 PHE A 390 TYR 0.015 0.002 TYR A 79 ARG 0.002 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.02827 ( 467) hydrogen bonds : angle 3.50394 ( 1329) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.37976 ( 4) covalent geometry : bond 0.00284 ( 6792) covalent geometry : angle 0.49516 ( 9218) ********************** 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 119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.766 Fit side-chains REVERT: A 93 ASN cc_start: 0.7648 (m110) cc_final: 0.7000 (m110) REVERT: A 154 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 310 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8035 (mm) REVERT: A 332 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8687 (tm-30) REVERT: A 348 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8816 (m) REVERT: A 353 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 548 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: B 310 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8064 (mm) REVERT: B 348 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8792 (m) REVERT: B 414 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7872 (tp) REVERT: B 548 GLU cc_start: 0.8334 (pm20) cc_final: 0.7848 (pm20) outliers start: 27 outliers final: 17 residues processed: 111 average time/residue: 0.1293 time to fit residues: 21.3634 Evaluate side-chains 116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 353 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 113 SER 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 348 SER 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: 0.9990 chunk 75 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.145670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115805 restraints weight = 7682.339| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.94 r_work: 0.3097 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.004 0.038 6794 Z= 0.144 Angle : 0.510 8.164 9222 Z= 0.266 Chirality : 0.036 0.128 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.739 21.242 896 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.60 % Allowed : 23.20 % 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: 3.27 (0.30), residues: 838 helix: 2.78 (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 0.009 0.001 TRP B 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 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 467) hydrogen bonds : angle 3.53000 ( 1329) SS BOND : bond 0.00342 ( 2) SS BOND : angle 1.55691 ( 4) covalent geometry : bond 0.00352 ( 6792) covalent geometry : angle 0.50870 ( 9218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3345.77 seconds wall clock time: 58 minutes 58.66 seconds (3538.66 seconds total)