Starting phenix.real_space_refine on Tue Mar 11 17:52:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rld_19339/03_2025/8rld_19339_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rld_19339/03_2025/8rld_19339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rld_19339/03_2025/8rld_19339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rld_19339/03_2025/8rld_19339.map" model { file = "/net/cci-nas-00/data/ceres_data/8rld_19339/03_2025/8rld_19339_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rld_19339/03_2025/8rld_19339_trim.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2107 2.51 5 N 524 2.21 5 O 559 1.98 5 H 3209 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6416 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6392 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.70, per 1000 atoms: 0.73 Number of scatterers: 6416 At special positions: 0 Unit cell: (54.988, 68.968, 81.084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 559 8.00 N 524 7.00 C 2107 6.00 H 3209 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 694.2 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 93.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 100 through 125 removed outlier: 4.533A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 163 removed outlier: 3.684A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 193 through 222 Proline residue: A 215 - end of helix removed outlier: 3.600A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 257 removed outlier: 4.460A pdb=" N LEU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 259 through 281 removed outlier: 3.760A pdb=" N LEU A 263 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.647A pdb=" N ILE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 312 through 347 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 360 through 390 removed outlier: 3.898A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 4.323A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 451 removed outlier: 3.577A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 525 removed outlier: 4.358A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.864A pdb=" N ASP A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 852 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: 2.45 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3201 1.03 - 1.23: 8 1.23 - 1.42: 1391 1.42 - 1.62: 1864 1.62 - 1.81: 26 Bond restraints: 6490 Sorted by residual: bond pdb=" C3' LMT A 601 " pdb=" O3' LMT A 601 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C7 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 1.529 1.489 0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C6' LMT A 601 " pdb=" O6' LMT A 601 " ideal model delta sigma weight residual 1.407 1.370 0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" C2 LMT A 601 " pdb=" C3 LMT A 601 " ideal model delta sigma weight residual 1.529 1.493 0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C8 LMT A 601 " pdb=" C9 LMT A 601 " ideal model delta sigma weight residual 1.531 1.496 0.035 2.00e-02 2.50e+03 3.09e+00 ... (remaining 6485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 11584 1.98 - 3.96: 76 3.96 - 5.94: 15 5.94 - 7.92: 1 7.92 - 9.90: 2 Bond angle restraints: 11678 Sorted by residual: angle pdb=" C2 LMT A 601 " pdb=" C3 LMT A 601 " pdb=" C4 LMT A 601 " ideal model delta sigma weight residual 117.09 107.19 9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 119.32 -5.72 1.90e+00 2.77e-01 9.07e+00 angle pdb=" C10 LMT A 601 " pdb=" C9 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 116.03 107.71 8.32 3.00e+00 1.11e-01 7.68e+00 angle pdb=" N TRP A 178 " pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " ideal model delta sigma weight residual 110.30 114.54 -4.24 1.54e+00 4.22e-01 7.59e+00 angle pdb=" C6 LMT A 601 " pdb=" C7 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 117.26 109.35 7.91 3.00e+00 1.11e-01 6.95e+00 ... (remaining 11673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 2772 16.00 - 32.00: 199 32.00 - 48.00: 43 48.00 - 64.01: 67 64.01 - 80.01: 2 Dihedral angle restraints: 3083 sinusoidal: 1617 harmonic: 1466 Sorted by residual: dihedral pdb=" CA THR A 392 " pdb=" C THR A 392 " pdb=" N GLN A 393 " pdb=" CA GLN A 393 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CG ARG A 342 " pdb=" CD ARG A 342 " pdb=" NE ARG A 342 " pdb=" CZ ARG A 342 " ideal model delta sinusoidal sigma weight residual -180.00 -137.42 -42.58 2 1.50e+01 4.44e-03 9.76e+00 dihedral pdb=" N LYS A 361 " pdb=" CA LYS A 361 " pdb=" CB LYS A 361 " pdb=" CG LYS A 361 " ideal model delta sinusoidal sigma weight residual -60.00 -112.13 52.13 3 1.50e+01 4.44e-03 9.08e+00 ... (remaining 3080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 424 0.044 - 0.088: 93 0.088 - 0.132: 10 0.132 - 0.176: 1 0.176 - 0.220: 3 Chirality restraints: 531 Sorted by residual: chirality pdb=" CB ILE A 247 " pdb=" CA ILE A 247 " pdb=" CG1 ILE A 247 " pdb=" CG2 ILE A 247 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C4' LMT A 601 " pdb=" C3' LMT A 601 " pdb=" C5' LMT A 601 " pdb=" O1B LMT A 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C5' LMT A 601 " pdb=" C4' LMT A 601 " pdb=" C6' LMT A 601 " pdb=" O5' LMT A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.31 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 528 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.022 2.00e-02 2.50e+03 1.33e-02 7.03e+00 pdb=" CG TRP A 178 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP A 178 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 178 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 387 " 0.014 2.00e-02 2.50e+03 1.30e-02 6.81e+00 pdb=" CG TRP A 387 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 387 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 387 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 387 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 387 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 387 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A 387 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 387 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 387 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 387 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 228 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C THR A 228 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 228 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 229 " 0.012 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 222 2.15 - 2.76: 12291 2.76 - 3.37: 19734 3.37 - 3.99: 24093 3.99 - 4.60: 38095 Nonbonded interactions: 94435 Sorted by model distance: nonbonded pdb=" O GLY A 206 " pdb=" HG SER A 209 " model vdw 1.535 2.450 nonbonded pdb=" O SER A 186 " pdb=" HD1 HIS A 260 " model vdw 1.652 2.450 nonbonded pdb=" O LEU A 161 " pdb=" H PHE A 165 " model vdw 1.680 2.450 nonbonded pdb=" O SER A 319 " pdb=" HG SER A 323 " model vdw 1.691 2.450 nonbonded pdb="HH12 ARG A 227 " pdb=" OG1 THR A 228 " model vdw 1.719 2.450 ... (remaining 94430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.890 Find NCS groups from input model: 0.050 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:15.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 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 0.041 3281 Z= 0.218 Angle : 0.595 9.898 4462 Z= 0.298 Chirality : 0.039 0.220 531 Planarity : 0.004 0.046 545 Dihedral : 12.393 80.008 1130 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.40), residues: 416 helix: 1.07 (0.26), residues: 371 sheet: None (None), residues: 0 loop : -0.34 (1.01), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 387 HIS 0.001 0.000 HIS A 341 PHE 0.009 0.001 PHE A 236 TYR 0.009 0.001 TYR A 160 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 1.2323 time to fit residues: 65.5914 Evaluate side-chains 43 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.220607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.210818 restraints weight = 10780.286| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 1.28 r_work: 0.4253 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 3281 Z= 0.318 Angle : 0.623 6.436 4462 Z= 0.342 Chirality : 0.038 0.137 531 Planarity : 0.006 0.062 545 Dihedral : 6.124 57.037 486 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.83 % Allowed : 8.84 % Favored : 89.33 % 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: 1.08 (0.39), residues: 416 helix: 0.98 (0.25), residues: 377 sheet: None (None), residues: 0 loop : -1.19 (0.95), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 178 HIS 0.005 0.002 HIS A 341 PHE 0.013 0.002 PHE A 193 TYR 0.012 0.002 TYR A 120 ARG 0.006 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.7056 (mtt) cc_final: 0.5871 (tmm) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 1.2881 time to fit residues: 89.8054 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 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 = 0.4349 r_free = 0.4349 target = 0.216056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.206303 restraints weight = 10975.098| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 1.33 r_work: 0.4222 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.4131 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 3281 Z= 0.298 Angle : 0.578 4.878 4462 Z= 0.322 Chirality : 0.037 0.131 531 Planarity : 0.005 0.047 545 Dihedral : 5.595 42.999 486 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.22 % Allowed : 11.89 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.39), residues: 416 helix: 1.13 (0.25), residues: 368 sheet: None (None), residues: 0 loop : -1.32 (0.83), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 178 HIS 0.006 0.002 HIS A 341 PHE 0.010 0.001 PHE A 193 TYR 0.013 0.002 TYR A 116 ARG 0.004 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.7133 (mtt) cc_final: 0.5909 (tmm) REVERT: A 334 MET cc_start: 0.8066 (ttt) cc_final: 0.7771 (tpt) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 1.4650 time to fit residues: 90.8939 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.214700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.204938 restraints weight = 11059.362| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 1.35 r_work: 0.4170 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4078 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 3281 Z= 0.308 Angle : 0.581 4.477 4462 Z= 0.329 Chirality : 0.038 0.133 531 Planarity : 0.005 0.051 545 Dihedral : 4.904 35.826 486 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.83 % Allowed : 14.02 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.39), residues: 416 helix: 1.05 (0.25), residues: 369 sheet: None (None), residues: 0 loop : -1.89 (0.82), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 178 HIS 0.006 0.002 HIS A 341 PHE 0.010 0.002 PHE A 193 TYR 0.013 0.002 TYR A 116 ARG 0.005 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.7138 (mtt) cc_final: 0.5958 (tmm) REVERT: A 334 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7806 (tpt) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 1.4074 time to fit residues: 86.0145 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.215313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.205234 restraints weight = 11074.175| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 1.38 r_work: 0.4178 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3281 Z= 0.275 Angle : 0.549 4.509 4462 Z= 0.311 Chirality : 0.037 0.122 531 Planarity : 0.005 0.052 545 Dihedral : 4.786 34.097 486 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.13 % Allowed : 14.94 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.39), residues: 416 helix: 1.18 (0.25), residues: 370 sheet: None (None), residues: 0 loop : -2.00 (0.81), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 178 HIS 0.005 0.002 HIS A 341 PHE 0.008 0.001 PHE A 222 TYR 0.012 0.001 TYR A 116 ARG 0.004 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.7174 (mtt) cc_final: 0.5977 (tmm) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 1.5235 time to fit residues: 88.1297 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.213428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.203360 restraints weight = 10921.930| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.38 r_work: 0.4143 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.4048 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 3281 Z= 0.309 Angle : 0.573 4.576 4462 Z= 0.328 Chirality : 0.038 0.136 531 Planarity : 0.005 0.054 545 Dihedral : 4.938 34.194 486 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.44 % Allowed : 14.94 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.39), residues: 416 helix: 1.10 (0.25), residues: 374 sheet: None (None), residues: 0 loop : -2.88 (0.80), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 178 HIS 0.006 0.002 HIS A 341 PHE 0.009 0.002 PHE A 430 TYR 0.013 0.002 TYR A 116 ARG 0.006 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.7117 (mtt) cc_final: 0.5903 (tmm) REVERT: A 455 ARG cc_start: 0.7691 (mtm180) cc_final: 0.7477 (mtm180) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 1.4502 time to fit residues: 88.6532 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.212098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.201599 restraints weight = 10945.940| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.43 r_work: 0.4136 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3281 Z= 0.259 Angle : 0.540 4.508 4462 Z= 0.307 Chirality : 0.036 0.126 531 Planarity : 0.005 0.053 545 Dihedral : 4.746 31.635 486 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.74 % Allowed : 15.24 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.40), residues: 416 helix: 1.23 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -3.01 (0.80), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.008 0.001 PHE A 327 TYR 0.012 0.001 TYR A 116 ARG 0.005 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.7134 (p) REVERT: A 306 MET cc_start: 0.7153 (mtt) cc_final: 0.5953 (tmm) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 1.5258 time to fit residues: 93.5543 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 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 = 0.4329 r_free = 0.4329 target = 0.213442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.203389 restraints weight = 10971.774| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 1.36 r_work: 0.4143 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 3281 Z= 0.300 Angle : 0.566 4.582 4462 Z= 0.324 Chirality : 0.038 0.137 531 Planarity : 0.005 0.054 545 Dihedral : 4.884 32.164 486 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.74 % Allowed : 15.55 % Favored : 81.71 % 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: 0.93 (0.39), residues: 416 helix: 1.05 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -3.14 (0.81), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 178 HIS 0.006 0.002 HIS A 341 PHE 0.010 0.002 PHE A 430 TYR 0.012 0.002 TYR A 116 ARG 0.004 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 209 SER cc_start: 0.7578 (OUTLIER) cc_final: 0.7167 (p) REVERT: A 306 MET cc_start: 0.7132 (mtt) cc_final: 0.5920 (tmm) outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 1.3935 time to fit residues: 83.7537 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.213342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.203267 restraints weight = 10999.571| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 1.38 r_work: 0.4153 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.4060 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3281 Z= 0.286 Angle : 0.560 4.539 4462 Z= 0.320 Chirality : 0.037 0.128 531 Planarity : 0.005 0.054 545 Dihedral : 4.815 31.320 486 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.44 % Allowed : 15.85 % Favored : 81.71 % 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: 0.97 (0.39), residues: 416 helix: 1.09 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -3.18 (0.81), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 178 HIS 0.006 0.002 HIS A 341 PHE 0.010 0.001 PHE A 430 TYR 0.012 0.002 TYR A 116 ARG 0.004 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.7558 (OUTLIER) cc_final: 0.7175 (p) REVERT: A 306 MET cc_start: 0.7160 (mtt) cc_final: 0.5921 (tmm) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 1.7105 time to fit residues: 104.2499 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 1 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.218341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.208483 restraints weight = 10942.739| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 1.31 r_work: 0.4229 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3281 Z= 0.213 Angle : 0.516 4.650 4462 Z= 0.291 Chirality : 0.036 0.122 531 Planarity : 0.005 0.054 545 Dihedral : 4.492 25.718 486 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.52 % Allowed : 17.07 % Favored : 81.40 % 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: 1.44 (0.40), residues: 416 helix: 1.40 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -3.17 (0.79), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.008 0.001 PHE A 234 TYR 0.010 0.001 TYR A 116 ARG 0.003 0.000 ARG A 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 168 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.469 Fit side-chains REVERT: A 209 SER cc_start: 0.7455 (OUTLIER) cc_final: 0.7131 (p) REVERT: A 306 MET cc_start: 0.7153 (mtt) cc_final: 0.6029 (tmm) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 1.3234 time to fit residues: 74.2566 Evaluate side-chains 51 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 496 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.217594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.208041 restraints weight = 11058.349| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 1.31 r_work: 0.4229 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3281 Z= 0.258 Angle : 0.541 4.562 4462 Z= 0.307 Chirality : 0.037 0.128 531 Planarity : 0.005 0.055 545 Dihedral : 4.634 29.079 486 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.13 % Allowed : 17.07 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.40), residues: 416 helix: 1.32 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -3.24 (0.78), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.008 0.001 PHE A 430 TYR 0.011 0.001 TYR A 116 ARG 0.004 0.000 ARG A 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5390.58 seconds wall clock time: 91 minutes 40.99 seconds (5500.99 seconds total)