Starting phenix.real_space_refine on Wed Sep 17 07:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6j_38988/09_2025/8y6j_38988_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6j_38988/09_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_38988/09_2025/8y6j_38988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6j_38988/09_2025/8y6j_38988.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6j_38988/09_2025/8y6j_38988_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6j_38988/09_2025/8y6j_38988_neut.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.35, per 1000 atoms: 0.35 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: 0.58 Conformation dependent library (CDL) restraints added in 387.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 1.06 Time building geometry restraints manager: 0.78 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: 0.01 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: 1.280 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.820 Find NCS groups from input model: 0.110 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG B 312 TYR 0.017 0.002 TYR B 79 PHE 0.013 0.001 PHE B 390 TRP 0.005 0.001 TRP A 134 HIS 0.009 0.002 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6792) covalent geometry : angle 0.54867 ( 9218) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.46700 ( 4) hydrogen bonds : bond 0.10107 ( 467) hydrogen bonds : angle 4.52647 ( 1329) *********************** 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 : 0.267 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: 0.0678 time to fit residues: 9.5846 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 : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.148210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.118604 restraints weight = 7616.615| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.91 r_work: 0.3123 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0560 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 : 0.497 7.021 9222 Z= 0.265 Chirality : 0.036 0.117 1106 Planarity : 0.003 0.031 1120 Dihedral : 3.679 19.830 896 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.41 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.15 (0.30), residues: 838 helix: 2.68 (0.20), residues: 616 sheet: None (None), residues: 0 loop : 0.38 (0.49), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.018 0.002 TYR A 79 PHE 0.013 0.001 PHE B 227 TRP 0.007 0.001 TRP B 134 HIS 0.005 0.002 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6792) covalent geometry : angle 0.49634 ( 9218) SS BOND : bond 0.00196 ( 2) SS BOND : angle 1.49739 ( 4) hydrogen bonds : bond 0.03227 ( 467) hydrogen bonds : angle 3.79226 ( 1329) *********************** 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 : 0.255 Fit side-chains REVERT: A 93 ASN cc_start: 0.7579 (m110) cc_final: 0.6980 (m110) REVERT: A 133 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7161 (mp) REVERT: B 107 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7272 (mp) REVERT: B 133 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7123 (mp) REVERT: B 414 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7873 (tp) REVERT: B 548 GLU cc_start: 0.8143 (pm20) cc_final: 0.7892 (pm20) outliers start: 22 outliers final: 6 residues processed: 111 average time/residue: 0.0622 time to fit residues: 10.1039 Evaluate side-chains 102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 107 LEU 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 65 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.147645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.118244 restraints weight = 7576.199| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.88 r_work: 0.3116 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6794 Z= 0.129 Angle : 0.488 5.990 9222 Z= 0.259 Chirality : 0.036 0.119 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.665 20.261 896 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.40 % Allowed : 23.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.14 (0.30), residues: 838 helix: 2.69 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.30 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.017 0.002 TYR A 79 PHE 0.013 0.001 PHE B 227 TRP 0.007 0.001 TRP B 134 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6792) covalent geometry : angle 0.48698 ( 9218) SS BOND : bond 0.00291 ( 2) SS BOND : angle 1.42823 ( 4) hydrogen bonds : bond 0.03015 ( 467) hydrogen bonds : angle 3.66640 ( 1329) *********************** 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: 18 poor density : 94 time to evaluate : 0.288 Fit side-chains REVERT: A 93 ASN cc_start: 0.7636 (m110) cc_final: 0.7021 (m110) REVERT: A 133 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7162 (mp) REVERT: B 107 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7258 (mp) REVERT: B 133 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7140 (mp) REVERT: B 414 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7896 (tp) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.0594 time to fit residues: 9.6845 Evaluate side-chains 105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 107 LEU 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 47 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.147083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.118384 restraints weight = 7658.308| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.79 r_work: 0.3114 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6794 Z= 0.137 Angle : 0.497 6.097 9222 Z= 0.262 Chirality : 0.036 0.122 1106 Planarity : 0.003 0.032 1120 Dihedral : 3.679 20.425 896 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.93 % Allowed : 22.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.30), residues: 838 helix: 2.69 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.27 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 312 TYR 0.017 0.002 TYR A 79 PHE 0.015 0.001 PHE A 390 TRP 0.007 0.001 TRP A 134 HIS 0.007 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6792) covalent geometry : angle 0.49635 ( 9218) SS BOND : bond 0.00298 ( 2) SS BOND : angle 1.44850 ( 4) hydrogen bonds : bond 0.02948 ( 467) hydrogen bonds : angle 3.61453 ( 1329) *********************** 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 112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.260 Fit side-chains REVERT: A 93 ASN cc_start: 0.7677 (m110) cc_final: 0.7064 (m110) REVERT: A 107 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7371 (mp) REVERT: A 133 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7259 (mp) REVERT: B 133 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7245 (mp) REVERT: B 310 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8175 (mm) REVERT: B 414 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7915 (tp) outliers start: 22 outliers final: 10 residues processed: 108 average time/residue: 0.0633 time to fit residues: 10.0533 Evaluate side-chains 104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 518 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.0170 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.0370 chunk 5 optimal weight: 0.5980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.149811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.120501 restraints weight = 7651.226| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.89 r_work: 0.3143 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6794 Z= 0.107 Angle : 0.475 6.792 9222 Z= 0.251 Chirality : 0.035 0.123 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.609 19.902 896 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.07 % Allowed : 23.33 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.28 (0.30), residues: 838 helix: 2.84 (0.20), residues: 616 sheet: None (None), residues: 0 loop : 0.24 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 312 TYR 0.016 0.001 TYR A 79 PHE 0.019 0.001 PHE A 390 TRP 0.006 0.001 TRP A 134 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6792) covalent geometry : angle 0.47470 ( 9218) SS BOND : bond 0.00224 ( 2) SS BOND : angle 1.22016 ( 4) hydrogen bonds : bond 0.02773 ( 467) hydrogen bonds : angle 3.49433 ( 1329) *********************** 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 119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.298 Fit side-chains REVERT: A 93 ASN cc_start: 0.7631 (m110) cc_final: 0.6942 (m110) REVERT: A 107 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7326 (mp) REVERT: A 133 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7109 (mp) REVERT: A 310 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8089 (mm) REVERT: B 133 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7127 (mp) REVERT: B 414 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7835 (tp) outliers start: 23 outliers final: 14 residues processed: 114 average time/residue: 0.0594 time to fit residues: 10.2984 Evaluate side-chains 110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 0.1980 chunk 57 optimal weight: 0.5980 chunk 18 optimal weight: 0.0000 chunk 63 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 0.0670 chunk 77 optimal weight: 0.9980 overall best weight: 0.3322 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.150612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.121274 restraints weight = 7607.251| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.91 r_work: 0.3152 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6794 Z= 0.104 Angle : 0.482 7.100 9222 Z= 0.252 Chirality : 0.035 0.123 1106 Planarity : 0.003 0.029 1120 Dihedral : 3.604 19.874 896 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.73 % Allowed : 22.67 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.32 (0.30), residues: 838 helix: 2.85 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.28 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.016 0.001 TYR A 79 PHE 0.018 0.001 PHE A 390 TRP 0.005 0.001 TRP B 134 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6792) covalent geometry : angle 0.48142 ( 9218) SS BOND : bond 0.00222 ( 2) SS BOND : angle 1.15150 ( 4) hydrogen bonds : bond 0.02767 ( 467) hydrogen bonds : angle 3.45020 ( 1329) *********************** 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 122 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.262 Fit side-chains REVERT: A 93 ASN cc_start: 0.7641 (m110) cc_final: 0.6889 (m110) REVERT: A 107 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7314 (mp) REVERT: A 133 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7146 (mp) REVERT: A 154 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.6830 (t80) REVERT: A 310 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 348 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8821 (m) REVERT: A 548 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: B 133 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7123 (mp) REVERT: B 310 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8133 (mm) REVERT: B 348 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8810 (m) REVERT: B 414 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7858 (tp) outliers start: 28 outliers final: 13 residues processed: 116 average time/residue: 0.0582 time to fit residues: 10.1264 Evaluate side-chains 112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 154 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 154 TYR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 518 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 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 = 0.3584 r_free = 0.3584 target = 0.147235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118733 restraints weight = 7490.746| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.76 r_work: 0.3121 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6794 Z= 0.143 Angle : 0.504 7.446 9222 Z= 0.263 Chirality : 0.036 0.128 1106 Planarity : 0.003 0.031 1120 Dihedral : 3.655 20.845 896 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.60 % Allowed : 22.53 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.29 (0.30), residues: 838 helix: 2.81 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.30 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.017 0.002 TYR A 79 PHE 0.016 0.001 PHE A 390 TRP 0.006 0.001 TRP A 134 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6792) covalent geometry : angle 0.50315 ( 9218) SS BOND : bond 0.00332 ( 2) SS BOND : angle 1.47261 ( 4) hydrogen bonds : bond 0.02879 ( 467) hydrogen bonds : angle 3.49519 ( 1329) *********************** 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 116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.251 Fit side-chains REVERT: A 93 ASN cc_start: 0.7599 (m110) cc_final: 0.6880 (m110) REVERT: A 107 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7380 (mp) REVERT: A 133 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7232 (mp) REVERT: A 154 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6795 (t80) REVERT: A 310 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8099 (mm) REVERT: A 333 HIS cc_start: 0.8120 (m90) cc_final: 0.7814 (m90) REVERT: A 344 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7674 (t) REVERT: A 348 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8866 (m) REVERT: A 548 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: B 133 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7263 (mp) REVERT: B 310 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8222 (mm) REVERT: B 348 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8845 (m) REVERT: B 414 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7923 (tp) outliers start: 27 outliers final: 16 residues processed: 109 average time/residue: 0.0589 time to fit residues: 9.6866 Evaluate side-chains 115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 344 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.146887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118412 restraints weight = 7594.090| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.78 r_work: 0.3115 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6794 Z= 0.138 Angle : 0.508 7.880 9222 Z= 0.264 Chirality : 0.036 0.128 1106 Planarity : 0.003 0.031 1120 Dihedral : 3.697 21.054 896 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.87 % Allowed : 22.40 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.34 (0.30), residues: 838 helix: 2.85 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.32 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.017 0.002 TYR A 79 PHE 0.016 0.001 PHE A 390 TRP 0.007 0.001 TRP A 134 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6792) covalent geometry : angle 0.50749 ( 9218) SS BOND : bond 0.00304 ( 2) SS BOND : angle 1.45660 ( 4) hydrogen bonds : bond 0.02886 ( 467) hydrogen bonds : angle 3.49682 ( 1329) *********************** 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 122 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.260 Fit side-chains REVERT: A 93 ASN cc_start: 0.7635 (m110) cc_final: 0.6967 (m110) REVERT: A 154 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 310 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8094 (mm) REVERT: A 333 HIS cc_start: 0.8245 (m90) cc_final: 0.7843 (m90) REVERT: A 344 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7659 (t) REVERT: A 348 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8867 (m) REVERT: A 548 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: B 133 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7268 (mp) REVERT: B 310 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8241 (mm) REVERT: B 348 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8833 (m) REVERT: B 414 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7911 (tp) REVERT: B 548 GLU cc_start: 0.8147 (pm20) cc_final: 0.7714 (pm20) outliers start: 29 outliers final: 15 residues processed: 114 average time/residue: 0.0567 time to fit residues: 9.7809 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 : 0.238 ------------------------------------------------------------------------------- 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 344 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.146602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.118006 restraints weight = 7637.132| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.79 r_work: 0.3110 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6794 Z= 0.142 Angle : 0.515 8.120 9222 Z= 0.268 Chirality : 0.036 0.126 1106 Planarity : 0.003 0.031 1120 Dihedral : 3.705 21.280 896 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.47 % Allowed : 22.80 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.35 (0.30), residues: 838 helix: 2.85 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.35 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.020 0.002 TYR A 339 PHE 0.016 0.001 PHE A 390 TRP 0.009 0.001 TRP A 134 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6792) covalent geometry : angle 0.51437 ( 9218) SS BOND : bond 0.00320 ( 2) SS BOND : angle 1.49586 ( 4) hydrogen bonds : bond 0.02909 ( 467) hydrogen bonds : angle 3.50942 ( 1329) *********************** 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: 26 poor density : 92 time to evaluate : 0.267 Fit side-chains REVERT: A 93 ASN cc_start: 0.7639 (m110) cc_final: 0.6985 (m110) REVERT: A 154 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.6742 (t80) REVERT: A 310 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8093 (mm) REVERT: A 333 HIS cc_start: 0.8295 (m90) cc_final: 0.7839 (m90) REVERT: A 344 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7685 (t) REVERT: A 348 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8861 (m) REVERT: A 548 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: B 133 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7266 (mp) REVERT: B 310 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8244 (mm) REVERT: B 348 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.8831 (m) REVERT: B 414 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7931 (tp) outliers start: 26 outliers final: 16 residues processed: 111 average time/residue: 0.0581 time to fit residues: 9.6453 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 : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 344 VAL 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 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 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 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.147877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119291 restraints weight = 7561.253| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.81 r_work: 0.3134 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6794 Z= 0.126 Angle : 0.509 8.396 9222 Z= 0.265 Chirality : 0.036 0.128 1106 Planarity : 0.003 0.030 1120 Dihedral : 3.685 20.865 896 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.47 % Allowed : 22.80 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.40 (0.30), residues: 838 helix: 2.89 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.37 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 312 TYR 0.016 0.002 TYR A 79 PHE 0.016 0.001 PHE A 390 TRP 0.008 0.001 TRP A 134 HIS 0.003 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6792) covalent geometry : angle 0.50827 ( 9218) SS BOND : bond 0.00268 ( 2) SS BOND : angle 1.36194 ( 4) hydrogen bonds : bond 0.02830 ( 467) hydrogen bonds : angle 3.46505 ( 1329) ********************** 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: 26 poor density : 93 time to evaluate : 0.254 Fit side-chains REVERT: A 93 ASN cc_start: 0.7639 (m110) cc_final: 0.6965 (m110) REVERT: A 154 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.6782 (t80) REVERT: A 310 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8074 (mm) REVERT: A 333 HIS cc_start: 0.8243 (m90) cc_final: 0.7739 (m90) REVERT: A 344 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7653 (t) REVERT: A 348 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8867 (m) REVERT: A 548 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: B 310 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8183 (mm) REVERT: B 348 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8823 (m) REVERT: B 414 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7907 (tp) REVERT: B 548 GLU cc_start: 0.8295 (pm20) cc_final: 0.7837 (pm20) outliers start: 26 outliers final: 16 residues processed: 112 average time/residue: 0.0593 time to fit residues: 10.0520 Evaluate side-chains 114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 344 VAL 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 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 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 32 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 30.0000 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.146264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117669 restraints weight = 7565.784| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.78 r_work: 0.3113 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6794 Z= 0.147 Angle : 0.521 8.185 9222 Z= 0.271 Chirality : 0.037 0.176 1106 Planarity : 0.003 0.031 1120 Dihedral : 3.727 21.338 896 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.60 % Allowed : 22.80 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.36 (0.30), residues: 838 helix: 2.85 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.38 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.017 0.002 TYR A 79 PHE 0.016 0.002 PHE A 390 TRP 0.009 0.001 TRP B 134 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6792) covalent geometry : angle 0.52001 ( 9218) SS BOND : bond 0.00340 ( 2) SS BOND : angle 1.52488 ( 4) hydrogen bonds : bond 0.02919 ( 467) hydrogen bonds : angle 3.49762 ( 1329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1667.69 seconds wall clock time: 29 minutes 26.21 seconds (1766.21 seconds total)