Starting phenix.real_space_refine on Wed Jul 23 16:50:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9v_63741/07_2025/9m9v_63741_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9v_63741/07_2025/9m9v_63741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m9v_63741/07_2025/9m9v_63741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9v_63741/07_2025/9m9v_63741.map" model { file = "/net/cci-nas-00/data/ceres_data/9m9v_63741/07_2025/9m9v_63741_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9v_63741/07_2025/9m9v_63741_neut_trim.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.075 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 P 1 5.49 5 S 30 5.16 5 C 2447 2.51 5 N 633 2.21 5 O 654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3765 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3747 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 26, 'TRANS': 469} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'5HG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.10, per 1000 atoms: 0.82 Number of scatterers: 3765 At special positions: 0 Unit cell: (104.384, 54.988, 68.968, 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 30 16.00 P 1 15.00 O 654 8.00 N 633 7.00 C 2447 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=1.73 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " 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: 0.99 Conformation dependent library (CDL) restraints added in 498.2 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 916 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 80.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 16 through 26 Processing helix chain 'A' and resid 28 through 36 removed outlier: 4.255A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.326A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.712A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.615A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.934A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 305 through 317 removed outlier: 4.705A pdb=" N SER A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 removed outlier: 3.904A pdb=" N LEU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.583A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 392 removed outlier: 3.521A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix removed outlier: 3.685A pdb=" N LEU A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.702A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.708A pdb=" N GLY A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 484 through 502 Proline residue: A 494 - end of helix removed outlier: 4.031A pdb=" N VAL A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.505A pdb=" N LEU A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 266 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 588 1.32 - 1.45: 1067 1.45 - 1.57: 2151 1.57 - 1.70: 0 1.70 - 1.83: 48 Bond restraints: 3854 Sorted by residual: bond pdb=" C CYS A 128 " pdb=" O CYS A 128 " ideal model delta sigma weight residual 1.243 1.205 0.039 9.50e-03 1.11e+04 1.65e+01 bond pdb=" C SER A 472 " pdb=" O SER A 472 " ideal model delta sigma weight residual 1.244 1.203 0.040 1.00e-02 1.00e+04 1.61e+01 bond pdb=" C THR A 424 " pdb=" O THR A 424 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.16e-02 7.43e+03 1.53e+01 bond pdb=" C PHE A 339 " pdb=" O PHE A 339 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.15e-02 7.56e+03 1.47e+01 bond pdb=" C GLN A 20 " pdb=" O GLN A 20 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.17e-02 7.31e+03 1.36e+01 ... (remaining 3849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 4713 2.11 - 4.23: 459 4.23 - 6.34: 62 6.34 - 8.46: 19 8.46 - 10.57: 5 Bond angle restraints: 5258 Sorted by residual: angle pdb=" N SER A 77 " pdb=" CA SER A 77 " pdb=" C SER A 77 " ideal model delta sigma weight residual 111.36 118.81 -7.45 1.09e+00 8.42e-01 4.67e+01 angle pdb=" N VAL A 143 " pdb=" CA VAL A 143 " pdb=" C VAL A 143 " ideal model delta sigma weight residual 110.62 104.48 6.14 1.02e+00 9.61e-01 3.62e+01 angle pdb=" N HIS A 48 " pdb=" CA HIS A 48 " pdb=" C HIS A 48 " ideal model delta sigma weight residual 109.24 100.48 8.76 1.51e+00 4.39e-01 3.36e+01 angle pdb=" N LEU A 313 " pdb=" CA LEU A 313 " pdb=" C LEU A 313 " ideal model delta sigma weight residual 112.54 105.71 6.83 1.22e+00 6.72e-01 3.13e+01 angle pdb=" N THR A 119 " pdb=" CA THR A 119 " pdb=" C THR A 119 " ideal model delta sigma weight residual 108.96 100.82 8.14 1.49e+00 4.50e-01 2.98e+01 ... (remaining 5253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 2090 17.53 - 35.05: 146 35.05 - 52.58: 20 52.58 - 70.10: 3 70.10 - 87.62: 2 Dihedral angle restraints: 2261 sinusoidal: 837 harmonic: 1424 Sorted by residual: dihedral pdb=" C ASN A 412 " pdb=" N ASN A 412 " pdb=" CA ASN A 412 " pdb=" CB ASN A 412 " ideal model delta harmonic sigma weight residual -122.60 -110.65 -11.95 0 2.50e+00 1.60e-01 2.28e+01 dihedral pdb=" N ARG A 15 " pdb=" C ARG A 15 " pdb=" CA ARG A 15 " pdb=" CB ARG A 15 " ideal model delta harmonic sigma weight residual 122.80 134.06 -11.26 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C ARG A 15 " pdb=" N ARG A 15 " pdb=" CA ARG A 15 " pdb=" CB ARG A 15 " ideal model delta harmonic sigma weight residual -122.60 -133.49 10.89 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 2258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 504 0.108 - 0.216: 99 0.216 - 0.323: 15 0.323 - 0.431: 3 0.431 - 0.539: 1 Chirality restraints: 622 Sorted by residual: chirality pdb=" CA ARG A 15 " pdb=" N ARG A 15 " pdb=" C ARG A 15 " pdb=" CB ARG A 15 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.26e+00 chirality pdb=" CA PHE A 152 " pdb=" N PHE A 152 " pdb=" C PHE A 152 " pdb=" CB PHE A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ASN A 412 " pdb=" N ASN A 412 " pdb=" C ASN A 412 " pdb=" CB ASN A 412 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 619 not shown) Planarity restraints: 655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO A 27 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 379 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 380 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 380 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 380 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO A 494 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " -0.034 5.00e-02 4.00e+02 ... (remaining 652 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1474 2.90 - 3.40: 3914 3.40 - 3.90: 6512 3.90 - 4.40: 7566 4.40 - 4.90: 12018 Nonbonded interactions: 31484 Sorted by model distance: nonbonded pdb=" N HIS A 48 " pdb=" O HIS A 48 " model vdw 2.402 2.496 nonbonded pdb=" N THR A 119 " pdb=" O THR A 119 " model vdw 2.406 2.496 nonbonded pdb=" N LEU A 313 " pdb=" N GLN A 314 " model vdw 2.548 2.560 nonbonded pdb=" N GLY A 393 " pdb=" O GLY A 393 " model vdw 2.555 2.496 nonbonded pdb=" N VAL A 365 " pdb=" O VAL A 365 " model vdw 2.563 2.496 ... (remaining 31479 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.012 0.306 3856 Z= 0.826 Angle : 1.403 10.571 5262 Z= 0.931 Chirality : 0.092 0.539 622 Planarity : 0.008 0.072 655 Dihedral : 12.130 87.624 1339 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.51 % Allowed : 3.31 % Favored : 96.18 % Cbeta Deviations : 0.44 % 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: -0.35 (0.36), residues: 488 helix: -0.31 (0.26), residues: 361 sheet: -0.61 (1.36), residues: 10 loop : 0.71 (0.59), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 346 HIS 0.007 0.002 HIS A 217 PHE 0.019 0.003 PHE A 374 TYR 0.025 0.003 TYR A 264 ARG 0.008 0.001 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.21060 ( 266) hydrogen bonds : angle 7.69276 ( 792) SS BOND : bond 0.21620 ( 2) SS BOND : angle 5.25853 ( 4) covalent geometry : bond 0.01054 ( 3854) covalent geometry : angle 1.39649 ( 5258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.417 Fit side-chains REVERT: A 112 ASP cc_start: 0.8190 (t0) cc_final: 0.7869 (t0) REVERT: A 306 MET cc_start: 0.7862 (mmm) cc_final: 0.7515 (mmt) REVERT: A 308 VAL cc_start: 0.8738 (t) cc_final: 0.8483 (p) REVERT: A 454 ARG cc_start: 0.7517 (ttt180) cc_final: 0.7274 (ttm110) REVERT: A 507 THR cc_start: 0.7148 (p) cc_final: 0.6800 (p) outliers start: 2 outliers final: 1 residues processed: 121 average time/residue: 0.1681 time to fit residues: 24.7621 Evaluate side-chains 75 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134877 restraints weight = 4358.959| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.39 r_work: 0.3458 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3856 Z= 0.167 Angle : 0.619 6.308 5262 Z= 0.328 Chirality : 0.041 0.146 622 Planarity : 0.006 0.048 655 Dihedral : 5.229 53.337 537 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.54 % Allowed : 10.18 % Favored : 87.28 % 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: 1.58 (0.39), residues: 488 helix: 1.13 (0.27), residues: 368 sheet: -1.43 (1.17), residues: 10 loop : 1.49 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.004 0.001 HIS A 275 PHE 0.014 0.002 PHE A 351 TYR 0.021 0.002 TYR A 264 ARG 0.003 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.05647 ( 266) hydrogen bonds : angle 4.89406 ( 792) SS BOND : bond 0.00794 ( 2) SS BOND : angle 1.16619 ( 4) covalent geometry : bond 0.00368 ( 3854) covalent geometry : angle 0.61792 ( 5258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.514 Fit side-chains REVERT: A 112 ASP cc_start: 0.8253 (t0) cc_final: 0.7973 (t0) REVERT: A 147 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8096 (tp) REVERT: A 308 VAL cc_start: 0.8791 (t) cc_final: 0.8511 (p) REVERT: A 398 GLN cc_start: 0.7542 (tp40) cc_final: 0.6906 (tp40) REVERT: A 442 PHE cc_start: 0.7502 (t80) cc_final: 0.7031 (t80) REVERT: A 458 MET cc_start: 0.8195 (mtp) cc_final: 0.7937 (mtp) outliers start: 10 outliers final: 3 residues processed: 84 average time/residue: 0.1289 time to fit residues: 14.1792 Evaluate side-chains 74 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131236 restraints weight = 4467.101| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.33 r_work: 0.3396 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3856 Z= 0.160 Angle : 0.575 5.546 5262 Z= 0.299 Chirality : 0.039 0.125 622 Planarity : 0.005 0.040 655 Dihedral : 4.950 56.969 536 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.05 % Allowed : 12.98 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.40), residues: 488 helix: 1.63 (0.27), residues: 367 sheet: -1.87 (1.29), residues: 10 loop : 0.97 (0.71), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.004 0.001 HIS A 275 PHE 0.016 0.002 PHE A 386 TYR 0.018 0.001 TYR A 264 ARG 0.003 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 266) hydrogen bonds : angle 4.50688 ( 792) SS BOND : bond 0.00831 ( 2) SS BOND : angle 0.77929 ( 4) covalent geometry : bond 0.00362 ( 3854) covalent geometry : angle 0.57524 ( 5258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.407 Fit side-chains REVERT: A 103 GLU cc_start: 0.7913 (pt0) cc_final: 0.7467 (pt0) REVERT: A 112 ASP cc_start: 0.8362 (t0) cc_final: 0.7878 (t0) REVERT: A 113 ASN cc_start: 0.7371 (p0) cc_final: 0.7032 (p0) REVERT: A 147 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8138 (tp) REVERT: A 163 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7570 (mtmm) REVERT: A 316 GLU cc_start: 0.7508 (mp0) cc_final: 0.7067 (mp0) REVERT: A 386 PHE cc_start: 0.8160 (t80) cc_final: 0.7848 (t80) REVERT: A 390 ASN cc_start: 0.8444 (m-40) cc_final: 0.8183 (m-40) REVERT: A 398 GLN cc_start: 0.7692 (tp40) cc_final: 0.6617 (tp40) REVERT: A 442 PHE cc_start: 0.7661 (t80) cc_final: 0.7210 (t80) REVERT: A 454 ARG cc_start: 0.7348 (ttt180) cc_final: 0.6739 (ttm110) REVERT: A 458 MET cc_start: 0.8299 (mtp) cc_final: 0.7968 (mtp) REVERT: A 482 TYR cc_start: 0.6465 (t80) cc_final: 0.6231 (t80) outliers start: 12 outliers final: 6 residues processed: 90 average time/residue: 0.1404 time to fit residues: 16.1098 Evaluate side-chains 82 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 507 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.0070 chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.165938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132376 restraints weight = 4406.103| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.36 r_work: 0.3414 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3856 Z= 0.134 Angle : 0.537 6.724 5262 Z= 0.274 Chirality : 0.037 0.124 622 Planarity : 0.004 0.036 655 Dihedral : 4.851 56.783 536 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.80 % Allowed : 15.01 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.40), residues: 488 helix: 1.99 (0.28), residues: 368 sheet: -2.04 (1.24), residues: 10 loop : 0.70 (0.71), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.003 0.001 HIS A 47 PHE 0.012 0.001 PHE A 351 TYR 0.011 0.001 TYR A 444 ARG 0.003 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 266) hydrogen bonds : angle 4.24856 ( 792) SS BOND : bond 0.00626 ( 2) SS BOND : angle 0.71500 ( 4) covalent geometry : bond 0.00291 ( 3854) covalent geometry : angle 0.53721 ( 5258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.987 Fit side-chains REVERT: A 103 GLU cc_start: 0.7902 (pt0) cc_final: 0.7480 (pt0) REVERT: A 112 ASP cc_start: 0.8353 (t0) cc_final: 0.7814 (t0) REVERT: A 113 ASN cc_start: 0.7175 (p0) cc_final: 0.6862 (p0) REVERT: A 147 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8121 (tp) REVERT: A 163 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7667 (mtmm) REVERT: A 316 GLU cc_start: 0.7478 (mp0) cc_final: 0.7023 (mp0) REVERT: A 417 GLN cc_start: 0.7791 (mp10) cc_final: 0.7552 (mp10) REVERT: A 442 PHE cc_start: 0.7619 (t80) cc_final: 0.7313 (t80) REVERT: A 454 ARG cc_start: 0.7355 (ttt180) cc_final: 0.6794 (ttm110) REVERT: A 458 MET cc_start: 0.8242 (mtp) cc_final: 0.7953 (mtp) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.1869 time to fit residues: 20.1593 Evaluate side-chains 84 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 507 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.0370 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 168 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133610 restraints weight = 4614.068| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.42 r_work: 0.3405 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3856 Z= 0.123 Angle : 0.526 5.529 5262 Z= 0.268 Chirality : 0.037 0.122 622 Planarity : 0.004 0.034 655 Dihedral : 4.750 57.267 536 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.54 % Allowed : 17.56 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.41), residues: 488 helix: 2.09 (0.28), residues: 368 sheet: -1.90 (1.27), residues: 10 loop : 0.70 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.003 0.001 HIS A 47 PHE 0.012 0.001 PHE A 351 TYR 0.008 0.001 TYR A 264 ARG 0.003 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 266) hydrogen bonds : angle 4.15266 ( 792) SS BOND : bond 0.00876 ( 2) SS BOND : angle 0.77994 ( 4) covalent geometry : bond 0.00260 ( 3854) covalent geometry : angle 0.52536 ( 5258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.734 Fit side-chains REVERT: A 46 THR cc_start: 0.8894 (m) cc_final: 0.8400 (p) REVERT: A 76 GLU cc_start: 0.8473 (tt0) cc_final: 0.8264 (tt0) REVERT: A 103 GLU cc_start: 0.7756 (pt0) cc_final: 0.7356 (pt0) REVERT: A 112 ASP cc_start: 0.8332 (t0) cc_final: 0.7864 (t0) REVERT: A 147 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8209 (tp) REVERT: A 163 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7691 (mtmm) REVERT: A 316 GLU cc_start: 0.7438 (mp0) cc_final: 0.6977 (mp0) REVERT: A 417 GLN cc_start: 0.7757 (mp10) cc_final: 0.7493 (mp10) REVERT: A 442 PHE cc_start: 0.7658 (t80) cc_final: 0.7296 (t80) REVERT: A 454 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6726 (ttm110) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.1701 time to fit residues: 18.5282 Evaluate side-chains 80 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 507 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131974 restraints weight = 4544.033| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.40 r_work: 0.3388 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3856 Z= 0.136 Angle : 0.535 6.340 5262 Z= 0.273 Chirality : 0.038 0.120 622 Planarity : 0.004 0.033 655 Dihedral : 4.758 58.252 536 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.54 % Allowed : 18.83 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.41), residues: 488 helix: 2.11 (0.28), residues: 370 sheet: -1.86 (1.31), residues: 10 loop : 0.79 (0.70), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 346 HIS 0.002 0.001 HIS A 275 PHE 0.019 0.001 PHE A 386 TYR 0.008 0.001 TYR A 264 ARG 0.002 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 266) hydrogen bonds : angle 4.12245 ( 792) SS BOND : bond 0.00785 ( 2) SS BOND : angle 0.40121 ( 4) covalent geometry : bond 0.00300 ( 3854) covalent geometry : angle 0.53520 ( 5258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 46 THR cc_start: 0.8875 (m) cc_final: 0.8377 (p) REVERT: A 76 GLU cc_start: 0.8562 (tt0) cc_final: 0.8056 (mm-30) REVERT: A 103 GLU cc_start: 0.7770 (pt0) cc_final: 0.7379 (pt0) REVERT: A 112 ASP cc_start: 0.8380 (t0) cc_final: 0.7936 (t0) REVERT: A 147 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 163 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7737 (mtmm) REVERT: A 316 GLU cc_start: 0.7531 (mp0) cc_final: 0.7022 (mp0) REVERT: A 417 GLN cc_start: 0.7857 (mp10) cc_final: 0.7530 (mp10) REVERT: A 442 PHE cc_start: 0.7696 (t80) cc_final: 0.7334 (t80) REVERT: A 454 ARG cc_start: 0.7323 (ttt180) cc_final: 0.6804 (ttm110) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.2170 time to fit residues: 22.3447 Evaluate side-chains 79 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130104 restraints weight = 4566.546| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.42 r_work: 0.3371 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3856 Z= 0.147 Angle : 0.529 5.421 5262 Z= 0.270 Chirality : 0.038 0.134 622 Planarity : 0.004 0.033 655 Dihedral : 4.771 59.294 536 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.29 % Allowed : 19.59 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.40), residues: 488 helix: 2.08 (0.28), residues: 370 sheet: -1.91 (1.32), residues: 10 loop : 0.72 (0.69), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 346 HIS 0.003 0.001 HIS A 275 PHE 0.014 0.001 PHE A 351 TYR 0.007 0.001 TYR A 354 ARG 0.003 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 266) hydrogen bonds : angle 4.08692 ( 792) SS BOND : bond 0.00764 ( 2) SS BOND : angle 0.42944 ( 4) covalent geometry : bond 0.00337 ( 3854) covalent geometry : angle 0.52890 ( 5258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.447 Fit side-chains REVERT: A 46 THR cc_start: 0.8877 (m) cc_final: 0.8386 (p) REVERT: A 76 GLU cc_start: 0.8628 (tt0) cc_final: 0.8131 (mm-30) REVERT: A 85 GLN cc_start: 0.8302 (mt0) cc_final: 0.8080 (mt0) REVERT: A 103 GLU cc_start: 0.7764 (pt0) cc_final: 0.7475 (pt0) REVERT: A 112 ASP cc_start: 0.8398 (t0) cc_final: 0.7986 (t0) REVERT: A 147 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8302 (tp) REVERT: A 163 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7830 (mtmm) REVERT: A 170 LEU cc_start: 0.8175 (tt) cc_final: 0.7939 (tp) REVERT: A 316 GLU cc_start: 0.7546 (mp0) cc_final: 0.7057 (mp0) REVERT: A 417 GLN cc_start: 0.7875 (mp10) cc_final: 0.7539 (mp10) REVERT: A 442 PHE cc_start: 0.7690 (t80) cc_final: 0.7338 (t80) REVERT: A 454 ARG cc_start: 0.7484 (ttt180) cc_final: 0.6906 (ttm110) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 0.1990 time to fit residues: 20.5507 Evaluate side-chains 81 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.166774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132668 restraints weight = 4502.589| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.38 r_work: 0.3390 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3856 Z= 0.130 Angle : 0.521 5.404 5262 Z= 0.264 Chirality : 0.037 0.121 622 Planarity : 0.004 0.033 655 Dihedral : 4.782 59.696 536 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.54 % Allowed : 19.85 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.41), residues: 488 helix: 2.17 (0.28), residues: 369 sheet: -1.85 (1.34), residues: 10 loop : 0.63 (0.70), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 PHE 0.022 0.001 PHE A 386 TYR 0.007 0.001 TYR A 444 ARG 0.003 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 266) hydrogen bonds : angle 4.02709 ( 792) SS BOND : bond 0.00639 ( 2) SS BOND : angle 0.46530 ( 4) covalent geometry : bond 0.00289 ( 3854) covalent geometry : angle 0.52058 ( 5258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.457 Fit side-chains REVERT: A 46 THR cc_start: 0.8845 (m) cc_final: 0.8341 (p) REVERT: A 76 GLU cc_start: 0.8552 (tt0) cc_final: 0.8050 (mm-30) REVERT: A 103 GLU cc_start: 0.7808 (pt0) cc_final: 0.7510 (pt0) REVERT: A 112 ASP cc_start: 0.8382 (t0) cc_final: 0.7993 (t0) REVERT: A 147 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8271 (tp) REVERT: A 170 LEU cc_start: 0.8106 (tt) cc_final: 0.7880 (tp) REVERT: A 316 GLU cc_start: 0.7600 (mp0) cc_final: 0.7109 (mp0) REVERT: A 417 GLN cc_start: 0.7920 (mp10) cc_final: 0.7586 (mp10) REVERT: A 442 PHE cc_start: 0.7700 (t80) cc_final: 0.7357 (t80) REVERT: A 452 MET cc_start: 0.8367 (ptp) cc_final: 0.8055 (pmm) REVERT: A 454 ARG cc_start: 0.7401 (ttt180) cc_final: 0.6901 (ttm110) outliers start: 10 outliers final: 5 residues processed: 83 average time/residue: 0.1375 time to fit residues: 14.7181 Evaluate side-chains 80 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.0000 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.163574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129672 restraints weight = 4476.521| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.43 r_work: 0.3388 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3856 Z= 0.127 Angle : 0.522 7.522 5262 Z= 0.261 Chirality : 0.037 0.121 622 Planarity : 0.004 0.034 655 Dihedral : 4.737 59.944 536 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.78 % Allowed : 21.37 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.41), residues: 488 helix: 2.20 (0.28), residues: 369 sheet: -1.65 (1.35), residues: 10 loop : 0.63 (0.71), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 346 HIS 0.002 0.001 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.007 0.001 TYR A 444 ARG 0.002 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 266) hydrogen bonds : angle 4.00356 ( 792) SS BOND : bond 0.00603 ( 2) SS BOND : angle 0.40832 ( 4) covalent geometry : bond 0.00282 ( 3854) covalent geometry : angle 0.52246 ( 5258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 1.645 Fit side-chains REVERT: A 46 THR cc_start: 0.8854 (m) cc_final: 0.8324 (p) REVERT: A 76 GLU cc_start: 0.8561 (tt0) cc_final: 0.7907 (mm-30) REVERT: A 103 GLU cc_start: 0.7695 (pt0) cc_final: 0.7407 (pt0) REVERT: A 112 ASP cc_start: 0.8359 (t0) cc_final: 0.7979 (t0) REVERT: A 147 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8233 (tp) REVERT: A 170 LEU cc_start: 0.8096 (tt) cc_final: 0.7877 (tp) REVERT: A 316 GLU cc_start: 0.7577 (mp0) cc_final: 0.7100 (mp0) REVERT: A 417 GLN cc_start: 0.7937 (mp10) cc_final: 0.7633 (mp10) REVERT: A 442 PHE cc_start: 0.7682 (t80) cc_final: 0.7360 (t80) REVERT: A 452 MET cc_start: 0.8377 (ptp) cc_final: 0.8078 (pmm) REVERT: A 454 ARG cc_start: 0.7399 (ttt180) cc_final: 0.6898 (ttm110) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.2044 time to fit residues: 20.6993 Evaluate side-chains 81 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.165570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129964 restraints weight = 4600.663| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.54 r_work: 0.3368 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3856 Z= 0.139 Angle : 0.545 7.451 5262 Z= 0.270 Chirality : 0.037 0.138 622 Planarity : 0.004 0.033 655 Dihedral : 4.725 59.137 536 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.13 % Rotamer: Outliers : 2.80 % Allowed : 20.87 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.40), residues: 488 helix: 2.11 (0.28), residues: 371 sheet: -1.51 (1.38), residues: 10 loop : 0.72 (0.71), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 346 HIS 0.002 0.001 HIS A 337 PHE 0.025 0.001 PHE A 386 TYR 0.007 0.001 TYR A 264 ARG 0.003 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 266) hydrogen bonds : angle 4.03776 ( 792) SS BOND : bond 0.00677 ( 2) SS BOND : angle 0.42915 ( 4) covalent geometry : bond 0.00316 ( 3854) covalent geometry : angle 0.54484 ( 5258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.548 Fit side-chains REVERT: A 46 THR cc_start: 0.8855 (m) cc_final: 0.8329 (p) REVERT: A 76 GLU cc_start: 0.8568 (tt0) cc_final: 0.7908 (mm-30) REVERT: A 103 GLU cc_start: 0.7633 (pt0) cc_final: 0.7375 (pt0) REVERT: A 112 ASP cc_start: 0.8381 (t0) cc_final: 0.8006 (t0) REVERT: A 147 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8260 (tp) REVERT: A 170 LEU cc_start: 0.8106 (tt) cc_final: 0.7890 (tp) REVERT: A 316 GLU cc_start: 0.7658 (mp0) cc_final: 0.7214 (mp0) REVERT: A 417 GLN cc_start: 0.7950 (mp10) cc_final: 0.7644 (mp10) REVERT: A 442 PHE cc_start: 0.7656 (t80) cc_final: 0.7379 (t80) REVERT: A 454 ARG cc_start: 0.7453 (ttt180) cc_final: 0.7210 (ttm-80) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.2058 time to fit residues: 21.5247 Evaluate side-chains 84 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131126 restraints weight = 4587.618| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.47 r_work: 0.3388 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3856 Z= 0.130 Angle : 0.533 7.731 5262 Z= 0.265 Chirality : 0.037 0.122 622 Planarity : 0.004 0.033 655 Dihedral : 4.676 58.723 536 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.13 % Rotamer: Outliers : 2.29 % Allowed : 22.39 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.41), residues: 488 helix: 2.18 (0.28), residues: 370 sheet: -1.46 (1.37), residues: 10 loop : 0.69 (0.72), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 346 HIS 0.002 0.001 HIS A 47 PHE 0.015 0.001 PHE A 351 TYR 0.007 0.001 TYR A 264 ARG 0.002 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 266) hydrogen bonds : angle 4.02798 ( 792) SS BOND : bond 0.00622 ( 2) SS BOND : angle 0.39888 ( 4) covalent geometry : bond 0.00289 ( 3854) covalent geometry : angle 0.53292 ( 5258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2421.18 seconds wall clock time: 45 minutes 33.85 seconds (2733.85 seconds total)