Starting phenix.real_space_refine on Thu Oct 22 19:17:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wty_66227/10_2026/9wty_66227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wty_66227/10_2026/9wty_66227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wty_66227/10_2026/9wty_66227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wty_66227/10_2026/9wty_66227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wty_66227/10_2026/9wty_66227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wty_66227/10_2026/9wty_66227.map" } resolution = 3.11 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= 0.000 sd= 0.020 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 25 5.16 5 C 2675 2.51 5 N 649 2.21 5 O 696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4045 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4045 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 23, 'TRANS': 486} Chain breaks: 1 Time building chain proxies: 0.62, per 1000 atoms: 0.15 Number of scatterers: 4045 At special positions: 0 Unit cell: (110.63, 74.037, 71.484, 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 25 16.00 O 696 8.00 N 649 7.00 C 2675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 136 " 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: 0.17 Conformation dependent library (CDL) restraints added in 82.6 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 70.0% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.559A pdb=" N VAL A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.590A pdb=" N PHE A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 43 removed outlier: 4.346A pdb=" N PHE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.556A pdb=" N ASN A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.570A pdb=" N TRP A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.921A pdb=" N SER A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.781A pdb=" N ILE A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 222 removed outlier: 3.913A pdb=" N MET A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 253 removed outlier: 3.729A pdb=" N ILE A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.895A pdb=" N PHE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.505A pdb=" N VAL A 271 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 289 through 305 Processing helix chain 'A' and resid 335 through 361 removed outlier: 3.915A pdb=" N ALA A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 394 removed outlier: 3.556A pdb=" N ALA A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Proline residue: A 383 - end of helix removed outlier: 4.010A pdb=" N THR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.508A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 449 removed outlier: 3.597A pdb=" N PHE A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 475 removed outlier: 3.538A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 487 through 507 removed outlier: 3.710A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 501 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE A 502 " --> pdb=" O VAL A 498 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 228 hydrogen bonds defined for protein. 666 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: 0.32 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1237 1.34 - 1.46: 939 1.46 - 1.58: 1931 1.58 - 1.69: 2 1.69 - 1.81: 43 Bond restraints: 4152 Sorted by residual: bond pdb=" CB PRO A 266 " pdb=" CG PRO A 266 " ideal model delta sigma weight residual 1.492 1.646 -0.154 5.00e-02 4.00e+02 9.49e+00 bond pdb=" CG PRO A 266 " pdb=" CD PRO A 266 " ideal model delta sigma weight residual 1.503 1.405 0.098 3.40e-02 8.65e+02 8.22e+00 bond pdb=" N PRO A 266 " pdb=" CD PRO A 266 " ideal model delta sigma weight residual 1.473 1.503 -0.030 1.40e-02 5.10e+03 4.56e+00 bond pdb=" N PRO A 266 " pdb=" CA PRO A 266 " ideal model delta sigma weight residual 1.469 1.443 0.026 1.28e-02 6.10e+03 4.18e+00 bond pdb=" CG PRO A 476 " pdb=" CD PRO A 476 " ideal model delta sigma weight residual 1.503 1.436 0.067 3.40e-02 8.65e+02 3.90e+00 ... (remaining 4147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 5627 3.54 - 7.08: 26 7.08 - 10.62: 2 10.62 - 14.16: 0 14.16 - 17.70: 1 Bond angle restraints: 5656 Sorted by residual: angle pdb=" CA PRO A 266 " pdb=" N PRO A 266 " pdb=" CD PRO A 266 " ideal model delta sigma weight residual 112.00 94.30 17.70 1.40e+00 5.10e-01 1.60e+02 angle pdb=" CA PRO A 476 " pdb=" N PRO A 476 " pdb=" CD PRO A 476 " ideal model delta sigma weight residual 112.00 102.87 9.13 1.40e+00 5.10e-01 4.25e+01 angle pdb=" N PRO A 266 " pdb=" CD PRO A 266 " pdb=" CG PRO A 266 " ideal model delta sigma weight residual 103.20 94.14 9.06 1.50e+00 4.44e-01 3.65e+01 angle pdb=" C LYS A 224 " pdb=" CA LYS A 224 " pdb=" CB LYS A 224 " ideal model delta sigma weight residual 116.34 110.20 6.14 1.40e+00 5.10e-01 1.92e+01 angle pdb=" N PRO A 476 " pdb=" CD PRO A 476 " pdb=" CG PRO A 476 " ideal model delta sigma weight residual 103.20 96.98 6.22 1.50e+00 4.44e-01 1.72e+01 ... (remaining 5651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 2019 17.09 - 34.19: 292 34.19 - 51.28: 85 51.28 - 68.37: 14 68.37 - 85.47: 3 Dihedral angle restraints: 2413 sinusoidal: 939 harmonic: 1474 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 113 " pdb=" CB CYS A 113 " ideal model delta sinusoidal sigma weight residual -86.00 -153.52 67.52 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS A 81 " pdb=" SG CYS A 81 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -126.41 40.41 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CA VAL A 265 " pdb=" C VAL A 265 " pdb=" N PRO A 266 " pdb=" CA PRO A 266 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 365 0.025 - 0.050: 167 0.050 - 0.074: 91 0.074 - 0.099: 25 0.099 - 0.124: 6 Chirality restraints: 654 Sorted by residual: chirality pdb=" CA VAL A 52 " pdb=" N VAL A 52 " pdb=" C VAL A 52 " pdb=" CB VAL A 52 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA ILE A 253 " pdb=" N ILE A 253 " pdb=" C ILE A 253 " pdb=" CB ILE A 253 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA PHE A 507 " pdb=" N PHE A 507 " pdb=" C PHE A 507 " pdb=" CB PHE A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 651 not shown) Planarity restraints: 699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 265 " 0.094 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PRO A 266 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 475 " 0.074 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO A 476 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 452 " -0.027 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 453 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.023 5.00e-02 4.00e+02 ... (remaining 696 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 156 2.72 - 3.27: 4116 3.27 - 3.81: 6572 3.81 - 4.36: 7519 4.36 - 4.90: 13131 Nonbonded interactions: 31494 Sorted by model distance: nonbonded pdb=" OD1 ASP A 362 " pdb=" OH TYR A 490 " model vdw 2.176 3.040 nonbonded pdb=" O TYR A 423 " pdb=" OG SER A 426 " model vdw 2.211 3.040 nonbonded pdb=" O LEU A 348 " pdb=" OG1 THR A 352 " model vdw 2.224 3.040 nonbonded pdb=" ND2 ASN A 32 " pdb=" O GLN A 207 " model vdw 2.317 3.120 nonbonded pdb=" NH1 ARG A 49 " pdb=" OE2 GLU A 118 " model vdw 2.337 3.120 ... (remaining 31489 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.150 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:0.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.004 0.154 4154 Z= 0.152 Angle : 0.657 17.697 5660 Z= 0.376 Chirality : 0.037 0.124 654 Planarity : 0.007 0.129 699 Dihedral : 17.327 85.468 1459 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 32.80 % Favored : 67.20 % 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 are not related in a simple way. whole: 0.11 (0.39), residues: 506 helix: 1.79 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -3.04 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.015 0.001 TYR A 490 PHE 0.013 0.001 PHE A 22 TRP 0.010 0.001 TRP A 117 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.15 ( 4152) covalent geometry : angle 0.65658 / 0.38 ( 5656) SS BOND : bond 0.00272 / 0.14 ( 2) SS BOND : angle 0.99767 / 0.42 ( 4) hydrogen bonds : bond 0.13187 / 9.06 ( 228) hydrogen bonds : angle 5.15697 / 3.73 ( 666) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.134 Fit side-chains REVERT: A 487 MET cc_start: 0.5701 (mtt) cc_final: 0.5355 (mtm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0592 time to fit residues: 4.5421 Evaluate side-chains 58 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [24, 48, 26, 2, 16, 32, 31, 25, 50, 19, 30] chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN A 416 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.174479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144721 restraints weight = 5092.184| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.55 r_work: 0.3631 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4154 Z= 0.159 Angle : 0.605 6.527 5660 Z= 0.321 Chirality : 0.040 0.130 654 Planarity : 0.005 0.059 699 Dihedral : 4.248 18.783 554 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.47 % Allowed : 28.02 % Favored : 66.51 % 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 are not related in a simple way. whole: 0.10 (0.38), residues: 506 helix: 1.55 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.80 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 282 TYR 0.014 0.001 TYR A 452 PHE 0.018 0.001 PHE A 22 TRP 0.011 0.001 TRP A 117 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 4152) covalent geometry : angle 0.60391 / 0.32 ( 5656) SS BOND : bond 0.00548 / 0.28 ( 2) SS BOND : angle 1.20316 / 0.56 ( 4) hydrogen bonds : bond 0.04626 / 2.92 ( 228) hydrogen bonds : angle 4.30393 / 3.09 ( 666) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 381 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: A 416 GLN cc_start: 0.5154 (OUTLIER) cc_final: 0.4646 (pm20) outliers start: 24 outliers final: 9 residues processed: 92 average time/residue: 0.0532 time to fit residues: 6.3357 Evaluate side-chains 78 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 474 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [1, 34, 30, 45, 47, 21, 0, 12, 39, 18, 48] chunk 1 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.175450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145769 restraints weight = 5005.981| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.55 r_work: 0.3640 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4154 Z= 0.144 Angle : 0.587 6.491 5660 Z= 0.313 Chirality : 0.040 0.134 654 Planarity : 0.004 0.055 699 Dihedral : 4.320 23.031 554 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.33 % Allowed : 28.70 % Favored : 66.97 % 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 are not related in a simple way. whole: 0.02 (0.38), residues: 506 helix: 1.45 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -2.76 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.014 0.001 TYR A 452 PHE 0.016 0.001 PHE A 22 TRP 0.014 0.001 TRP A 117 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 4152) covalent geometry : angle 0.58637 / 0.31 ( 5656) SS BOND : bond 0.00429 / 0.22 ( 2) SS BOND : angle 1.21234 / 0.50 ( 4) hydrogen bonds : bond 0.04335 / 2.70 ( 228) hydrogen bonds : angle 4.17287 / 3.01 ( 666) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.7010 (mt) REVERT: A 379 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8084 (mm) REVERT: A 381 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 416 GLN cc_start: 0.5153 (OUTLIER) cc_final: 0.4844 (pp30) outliers start: 19 outliers final: 10 residues processed: 81 average time/residue: 0.0558 time to fit residues: 5.8914 Evaluate side-chains 76 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 474 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [23, 39, 30, 8, 42, 34, 14, 40, 3, 28, 36] chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 0.0070 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.176689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147186 restraints weight = 5028.528| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.56 r_work: 0.3654 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4154 Z= 0.129 Angle : 0.563 6.456 5660 Z= 0.299 Chirality : 0.039 0.141 654 Planarity : 0.004 0.049 699 Dihedral : 4.237 22.982 554 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.33 % Allowed : 28.47 % Favored : 67.20 % 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 are not related in a simple way. whole: 0.10 (0.38), residues: 506 helix: 1.52 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.77 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 282 TYR 0.011 0.001 TYR A 452 PHE 0.015 0.001 PHE A 22 TRP 0.013 0.001 TRP A 117 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 4152) covalent geometry : angle 0.56176 / 0.30 ( 5656) SS BOND : bond 0.00421 / 0.22 ( 2) SS BOND : angle 1.41731 / 0.56 ( 4) hydrogen bonds : bond 0.04001 / 2.49 ( 228) hydrogen bonds : angle 4.05916 / 2.93 ( 666) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 97 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7079 (mt) REVERT: A 108 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.6047 (mm) REVERT: A 254 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6004 (mmp80) REVERT: A 379 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8041 (mm) REVERT: A 381 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7293 (mt-10) outliers start: 19 outliers final: 9 residues processed: 83 average time/residue: 0.0662 time to fit residues: 6.9553 Evaluate side-chains 74 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 416 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [15, 40, 17, 12, 42, 46, 35, 0, 47, 33, 31] chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.173633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143997 restraints weight = 5070.145| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.56 r_work: 0.3616 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4154 Z= 0.163 Angle : 0.604 6.471 5660 Z= 0.320 Chirality : 0.041 0.139 654 Planarity : 0.004 0.047 699 Dihedral : 4.351 24.332 554 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.24 % Allowed : 28.47 % Favored : 66.29 % 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 are not related in a simple way. whole: -0.08 (0.38), residues: 506 helix: 1.39 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -2.88 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.013 0.001 TYR A 452 PHE 0.018 0.001 PHE A 22 TRP 0.012 0.001 TRP A 117 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 4152) covalent geometry : angle 0.60266 / 0.32 ( 5656) SS BOND : bond 0.00520 / 0.27 ( 2) SS BOND : angle 1.43775 / 0.60 ( 4) hydrogen bonds : bond 0.04455 / 2.79 ( 228) hydrogen bonds : angle 4.16152 / 3.01 ( 666) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7467 (mm) cc_final: 0.7166 (mm) REVERT: A 97 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7129 (mt) REVERT: A 254 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.5885 (mmp80) REVERT: A 379 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8069 (mm) REVERT: A 381 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7324 (mt-10) REVERT: A 416 GLN cc_start: 0.5018 (OUTLIER) cc_final: 0.4754 (pp30) outliers start: 23 outliers final: 12 residues processed: 84 average time/residue: 0.0499 time to fit residues: 5.5746 Evaluate side-chains 79 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 474 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [33, 34, 19, 8, 23, 46, 15, 48, 31, 40, 41] chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.176256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146440 restraints weight = 5079.181| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.58 r_work: 0.3642 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4154 Z= 0.128 Angle : 0.573 6.446 5660 Z= 0.303 Chirality : 0.039 0.145 654 Planarity : 0.004 0.045 699 Dihedral : 4.286 23.767 554 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.78 % Allowed : 28.93 % Favored : 66.29 % 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 are not related in a simple way. whole: 0.07 (0.38), residues: 506 helix: 1.50 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.79 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 282 TYR 0.011 0.001 TYR A 452 PHE 0.015 0.001 PHE A 22 TRP 0.011 0.001 TRP A 117 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 4152) covalent geometry : angle 0.57239 / 0.30 ( 5656) SS BOND : bond 0.00424 / 0.22 ( 2) SS BOND : angle 1.20085 / 0.50 ( 4) hydrogen bonds : bond 0.04015 / 2.50 ( 228) hydrogen bonds : angle 4.06600 / 2.94 ( 666) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7486 (mm) cc_final: 0.7239 (mm) REVERT: A 97 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7267 (mt) REVERT: A 121 GLN cc_start: 0.5652 (mm-40) cc_final: 0.5449 (mm-40) REVERT: A 254 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6065 (mmp80) REVERT: A 379 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 381 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7280 (mt-10) outliers start: 21 outliers final: 14 residues processed: 87 average time/residue: 0.0625 time to fit residues: 6.9772 Evaluate side-chains 81 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [3, 47, 45, 20, 15, 44, 24, 9, 23, 33, 35] chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.174433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144598 restraints weight = 5216.399| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.54 r_work: 0.3640 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4154 Z= 0.146 Angle : 0.591 6.471 5660 Z= 0.312 Chirality : 0.040 0.146 654 Planarity : 0.004 0.044 699 Dihedral : 4.307 23.859 554 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.01 % Allowed : 29.16 % Favored : 65.83 % 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 are not related in a simple way. whole: -0.04 (0.38), residues: 506 helix: 1.41 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -2.85 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 282 TYR 0.017 0.001 TYR A 490 PHE 0.017 0.001 PHE A 22 TRP 0.011 0.001 TRP A 117 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 4152) covalent geometry : angle 0.59035 / 0.31 ( 5656) SS BOND : bond 0.00492 / 0.25 ( 2) SS BOND : angle 1.22554 / 0.53 ( 4) hydrogen bonds : bond 0.04205 / 2.63 ( 228) hydrogen bonds : angle 4.11885 / 2.99 ( 666) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7595 (mm) cc_final: 0.7360 (mm) REVERT: A 97 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7279 (mt) REVERT: A 254 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6095 (mmp80) REVERT: A 379 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 381 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7273 (mt-10) outliers start: 22 outliers final: 17 residues processed: 83 average time/residue: 0.0508 time to fit residues: 5.6014 Evaluate side-chains 82 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 517 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [28, 10, 45, 42, 30, 13, 40, 1, 11, 24, 38] chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.174559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144969 restraints weight = 5037.439| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.51 r_work: 0.3645 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4154 Z= 0.139 Angle : 0.586 6.458 5660 Z= 0.310 Chirality : 0.040 0.143 654 Planarity : 0.004 0.043 699 Dihedral : 4.305 23.778 554 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.24 % Allowed : 29.38 % Favored : 65.38 % 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 are not related in a simple way. whole: 0.01 (0.38), residues: 506 helix: 1.46 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -2.86 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 282 TYR 0.011 0.001 TYR A 452 PHE 0.016 0.001 PHE A 22 TRP 0.011 0.001 TRP A 117 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4152) covalent geometry : angle 0.58524 / 0.31 ( 5656) SS BOND : bond 0.00478 / 0.24 ( 2) SS BOND : angle 1.18596 / 0.51 ( 4) hydrogen bonds : bond 0.04143 / 2.59 ( 228) hydrogen bonds : angle 4.09526 / 2.97 ( 666) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7585 (mm) cc_final: 0.7362 (mm) REVERT: A 97 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7285 (mt) REVERT: A 254 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6129 (mmp80) REVERT: A 379 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8165 (mm) REVERT: A 381 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7266 (mt-10) REVERT: A 416 GLN cc_start: 0.5230 (OUTLIER) cc_final: 0.4250 (mm110) REVERT: A 490 TYR cc_start: 0.5230 (m-80) cc_final: 0.4937 (m-80) outliers start: 23 outliers final: 14 residues processed: 86 average time/residue: 0.0672 time to fit residues: 7.3296 Evaluate side-chains 80 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 517 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [39, 14, 15, 46, 3, 22, 16, 35, 18, 5, 44] chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 3 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 0.0010 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 0.0670 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149076 restraints weight = 5157.985| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.55 r_work: 0.3691 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4154 Z= 0.118 Angle : 0.567 6.424 5660 Z= 0.298 Chirality : 0.039 0.154 654 Planarity : 0.004 0.045 699 Dihedral : 4.199 23.275 554 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.64 % Allowed : 30.98 % Favored : 65.38 % 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 are not related in a simple way. whole: 0.09 (0.38), residues: 506 helix: 1.55 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.86 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 282 TYR 0.010 0.001 TYR A 452 PHE 0.010 0.001 PHE A 22 TRP 0.011 0.001 TRP A 117 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 4152) covalent geometry : angle 0.56601 / 0.30 ( 5656) SS BOND : bond 0.00242 / 0.13 ( 2) SS BOND : angle 1.42810 / 0.56 ( 4) hydrogen bonds : bond 0.03618 / 2.24 ( 228) hydrogen bonds : angle 3.95015 / 2.86 ( 666) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7580 (mm) cc_final: 0.7368 (mm) REVERT: A 51 ARG cc_start: 0.7822 (ttt180) cc_final: 0.7296 (ttp80) REVERT: A 379 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8131 (mm) REVERT: A 381 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7246 (mt-10) outliers start: 16 outliers final: 9 residues processed: 74 average time/residue: 0.0652 time to fit residues: 6.1428 Evaluate side-chains 72 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 517 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [39, 37, 14, 9, 27, 48, 2, 30, 15, 7, 46] chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.0060 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 46 optimal weight: 0.0670 overall best weight: 0.4934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.176903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147235 restraints weight = 5023.994| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.51 r_work: 0.3671 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4154 Z= 0.133 Angle : 0.592 7.429 5660 Z= 0.309 Chirality : 0.039 0.152 654 Planarity : 0.004 0.045 699 Dihedral : 4.237 23.858 554 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.51 % Allowed : 31.21 % Favored : 66.29 % 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 are not related in a simple way. whole: 0.07 (0.38), residues: 506 helix: 1.53 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -2.83 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 282 TYR 0.011 0.001 TYR A 423 PHE 0.015 0.001 PHE A 22 TRP 0.011 0.001 TRP A 117 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 4152) covalent geometry : angle 0.59119 / 0.31 ( 5656) SS BOND : bond 0.00398 / 0.21 ( 2) SS BOND : angle 1.31600 / 0.53 ( 4) hydrogen bonds : bond 0.03890 / 2.42 ( 228) hydrogen bonds : angle 3.98157 / 2.88 ( 666) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7593 (mm) cc_final: 0.7372 (mm) REVERT: A 379 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8164 (mm) REVERT: A 381 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7266 (mt-10) outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.0632 time to fit residues: 5.9223 Evaluate side-chains 72 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 517 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [9, 41, 4, 31, 17, 24, 20, 29, 5, 27, 44] chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.176935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.147103 restraints weight = 5079.194| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.53 r_work: 0.3675 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.197 4154 Z= 0.268 Angle : 1.198 59.186 5660 Z= 0.698 Chirality : 0.043 0.439 654 Planarity : 0.004 0.045 699 Dihedral : 4.237 23.847 554 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.05 % Allowed : 31.44 % Favored : 66.51 % Cbeta Deviations : 0.21 % 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 are not related in a simple way. whole: 0.06 (0.38), residues: 506 helix: 1.53 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -2.84 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 282 TYR 0.011 0.001 TYR A 452 PHE 0.015 0.001 PHE A 22 TRP 0.011 0.001 TRP A 117 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.27 ( 4152) covalent geometry : angle 1.19832 / 0.70 ( 5656) SS BOND : bond 0.00431 / 0.22 ( 2) SS BOND : angle 1.26743 / 0.51 ( 4) hydrogen bonds : bond 0.03902 / 2.43 ( 228) hydrogen bonds : angle 3.98416 / 2.88 ( 666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1127.09 seconds wall clock time: 19 minutes 51.57 seconds (1191.57 seconds total)