Starting phenix.real_space_refine on Wed Sep 17 04:10:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9v_63741/09_2025/9m9v_63741_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9v_63741/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9m9v_63741/09_2025/9m9v_63741_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9v_63741/09_2025/9m9v_63741_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m9v_63741/09_2025/9m9v_63741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9v_63741/09_2025/9m9v_63741.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.075 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1, 'GLU:plan': 4} 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: 1.24, per 1000 atoms: 0.33 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: 0.41 Conformation dependent library (CDL) restraints added in 166.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.13 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: 0.59 Time building geometry restraints manager: 0.47 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: 1.250 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.070 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG A 394 TYR 0.025 0.003 TYR A 264 PHE 0.019 0.003 PHE A 374 TRP 0.016 0.002 TRP A 346 HIS 0.007 0.002 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.01054 ( 3854) covalent geometry : angle 1.39649 ( 5258) SS BOND : bond 0.21620 ( 2) SS BOND : angle 5.25853 ( 4) hydrogen bonds : bond 0.21060 ( 266) hydrogen bonds : angle 7.69276 ( 792) *********************** 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 : 0.167 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: 0.8484 (p) REVERT: A 454 ARG cc_start: 0.7517 (ttt180) cc_final: 0.7275 (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: 0.0810 time to fit residues: 11.9026 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 : 0.145 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.169672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135506 restraints weight = 4427.936| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.39 r_work: 0.3451 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3856 Z= 0.168 Angle : 0.633 6.539 5262 Z= 0.334 Chirality : 0.041 0.142 622 Planarity : 0.006 0.047 655 Dihedral : 5.231 53.032 537 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.04 % Allowed : 10.43 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.39), residues: 488 helix: 1.18 (0.27), residues: 368 sheet: -1.43 (1.16), residues: 10 loop : 1.48 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 395 TYR 0.022 0.002 TYR A 264 PHE 0.015 0.002 PHE A 351 TRP 0.011 0.001 TRP A 346 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3854) covalent geometry : angle 0.63188 ( 5258) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.40697 ( 4) hydrogen bonds : bond 0.05728 ( 266) hydrogen bonds : angle 4.89452 ( 792) *********************** 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 83 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.140 Fit side-chains REVERT: A 112 ASP cc_start: 0.8203 (t0) cc_final: 0.7905 (t0) REVERT: A 147 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7971 (tp) REVERT: A 308 VAL cc_start: 0.8782 (t) cc_final: 0.8500 (p) REVERT: A 398 GLN cc_start: 0.7499 (tp40) cc_final: 0.6920 (tp40) REVERT: A 442 PHE cc_start: 0.7404 (t80) cc_final: 0.6957 (t80) REVERT: A 458 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7779 (mtp) outliers start: 8 outliers final: 3 residues processed: 81 average time/residue: 0.0606 time to fit residues: 6.3580 Evaluate side-chains 72 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.164180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129383 restraints weight = 4529.642| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.40 r_work: 0.3376 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3856 Z= 0.170 Angle : 0.589 5.750 5262 Z= 0.305 Chirality : 0.040 0.127 622 Planarity : 0.005 0.039 655 Dihedral : 4.979 57.005 536 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.40), residues: 488 helix: 1.61 (0.27), residues: 368 sheet: -1.84 (1.30), residues: 10 loop : 0.98 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 286 TYR 0.018 0.001 TYR A 264 PHE 0.016 0.002 PHE A 386 TRP 0.012 0.001 TRP A 274 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 3854) covalent geometry : angle 0.58863 ( 5258) SS BOND : bond 0.00866 ( 2) SS BOND : angle 0.77819 ( 4) hydrogen bonds : bond 0.04988 ( 266) hydrogen bonds : angle 4.49584 ( 792) *********************** 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 : 0.144 Fit side-chains REVERT: A 103 GLU cc_start: 0.7896 (pt0) cc_final: 0.7506 (pt0) REVERT: A 112 ASP cc_start: 0.8387 (t0) cc_final: 0.7885 (t0) REVERT: A 113 ASN cc_start: 0.7372 (p0) cc_final: 0.7026 (p0) REVERT: A 147 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8185 (mt) REVERT: A 163 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7581 (mtmm) REVERT: A 316 GLU cc_start: 0.7541 (mp0) cc_final: 0.7080 (mp0) REVERT: A 386 PHE cc_start: 0.8200 (t80) cc_final: 0.7895 (t80) REVERT: A 390 ASN cc_start: 0.8448 (m-40) cc_final: 0.8151 (m-40) REVERT: A 398 GLN cc_start: 0.7708 (tp40) cc_final: 0.6800 (tp40) REVERT: A 442 PHE cc_start: 0.7643 (t80) cc_final: 0.7214 (t80) REVERT: A 454 ARG cc_start: 0.7337 (ttt180) cc_final: 0.6743 (ttm110) REVERT: A 482 TYR cc_start: 0.6470 (t80) cc_final: 0.6230 (t80) outliers start: 12 outliers final: 6 residues processed: 90 average time/residue: 0.0652 time to fit residues: 7.4440 Evaluate side-chains 81 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 LEU 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 32 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** 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 = 0.3916 r_free = 0.3916 target = 0.164661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129891 restraints weight = 4517.697| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.33 r_work: 0.3382 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3856 Z= 0.154 Angle : 0.559 5.577 5262 Z= 0.286 Chirality : 0.039 0.126 622 Planarity : 0.005 0.036 655 Dihedral : 4.929 57.472 536 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.54 % Allowed : 16.03 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.40), residues: 488 helix: 1.97 (0.28), residues: 362 sheet: -1.94 (1.27), residues: 10 loop : 0.74 (0.68), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.011 0.001 TYR A 264 PHE 0.012 0.001 PHE A 351 TRP 0.012 0.001 TRP A 274 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3854) covalent geometry : angle 0.55859 ( 5258) SS BOND : bond 0.00713 ( 2) SS BOND : angle 0.73258 ( 4) hydrogen bonds : bond 0.04728 ( 266) hydrogen bonds : angle 4.31896 ( 792) *********************** 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 80 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.110 Fit side-chains REVERT: A 103 GLU cc_start: 0.7893 (pt0) cc_final: 0.7389 (pt0) REVERT: A 112 ASP cc_start: 0.8516 (t0) cc_final: 0.8018 (t0) REVERT: A 113 ASN cc_start: 0.7308 (p0) cc_final: 0.7004 (p0) REVERT: A 163 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7783 (mtmm) REVERT: A 316 GLU cc_start: 0.7525 (mp0) cc_final: 0.7072 (mp0) REVERT: A 386 PHE cc_start: 0.8165 (t80) cc_final: 0.7772 (t80) REVERT: A 390 ASN cc_start: 0.8555 (m-40) cc_final: 0.8204 (m-40) REVERT: A 398 GLN cc_start: 0.7901 (tp40) cc_final: 0.7572 (tp40) REVERT: A 417 GLN cc_start: 0.7810 (mp10) cc_final: 0.7533 (mp10) REVERT: A 442 PHE cc_start: 0.7685 (t80) cc_final: 0.7343 (t80) REVERT: A 454 ARG cc_start: 0.7517 (ttt180) cc_final: 0.6947 (ttm110) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.0612 time to fit residues: 5.8977 Evaluate side-chains 77 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 448 LEU 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 38 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 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 = 0.3931 r_free = 0.3931 target = 0.166261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130716 restraints weight = 4513.918| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.46 r_work: 0.3391 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3959 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= 0.128 Angle : 0.532 8.267 5262 Z= 0.269 Chirality : 0.037 0.120 622 Planarity : 0.004 0.035 655 Dihedral : 4.801 58.020 536 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.54 % Allowed : 16.54 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.40), residues: 488 helix: 2.18 (0.28), residues: 362 sheet: -1.64 (1.30), residues: 10 loop : 0.72 (0.68), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 394 TYR 0.009 0.001 TYR A 354 PHE 0.014 0.001 PHE A 351 TRP 0.011 0.001 TRP A 274 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3854) covalent geometry : angle 0.53163 ( 5258) SS BOND : bond 0.01114 ( 2) SS BOND : angle 0.44620 ( 4) hydrogen bonds : bond 0.04332 ( 266) hydrogen bonds : angle 4.14010 ( 792) *********************** 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 89 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.146 Fit side-chains REVERT: A 46 THR cc_start: 0.8885 (m) cc_final: 0.8388 (p) REVERT: A 103 GLU cc_start: 0.7772 (pt0) cc_final: 0.7330 (pt0) REVERT: A 112 ASP cc_start: 0.8385 (t0) cc_final: 0.7886 (t0) REVERT: A 113 ASN cc_start: 0.7243 (p0) cc_final: 0.6760 (p0) REVERT: A 163 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7781 (mtmm) REVERT: A 316 GLU cc_start: 0.7468 (mp0) cc_final: 0.6991 (mp0) REVERT: A 417 GLN cc_start: 0.7832 (mp10) cc_final: 0.7558 (mp10) REVERT: A 442 PHE cc_start: 0.7653 (t80) cc_final: 0.7353 (t80) REVERT: A 454 ARG cc_start: 0.7368 (ttt180) cc_final: 0.6809 (ttm110) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.0608 time to fit residues: 6.6633 Evaluate side-chains 78 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 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 40 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.0020 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 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 = 0.3923 r_free = 0.3923 target = 0.166140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131495 restraints weight = 4532.172| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.40 r_work: 0.3373 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3856 Z= 0.140 Angle : 0.542 7.267 5262 Z= 0.276 Chirality : 0.038 0.120 622 Planarity : 0.004 0.034 655 Dihedral : 4.831 58.877 536 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.04 % Allowed : 18.83 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.41), residues: 488 helix: 2.19 (0.28), residues: 364 sheet: -1.75 (1.34), residues: 10 loop : 0.85 (0.68), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 394 TYR 0.010 0.001 TYR A 354 PHE 0.014 0.001 PHE A 351 TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3854) covalent geometry : angle 0.54251 ( 5258) SS BOND : bond 0.00811 ( 2) SS BOND : angle 0.41174 ( 4) hydrogen bonds : bond 0.04401 ( 266) hydrogen bonds : angle 4.13162 ( 792) *********************** 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: 8 poor density : 77 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 46 THR cc_start: 0.8884 (m) cc_final: 0.8388 (p) REVERT: A 103 GLU cc_start: 0.7832 (pt0) cc_final: 0.7462 (pt0) REVERT: A 112 ASP cc_start: 0.8418 (t0) cc_final: 0.7976 (t0) REVERT: A 163 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7770 (mtmm) REVERT: A 316 GLU cc_start: 0.7534 (mp0) cc_final: 0.7045 (mp0) REVERT: A 417 GLN cc_start: 0.7851 (mp10) cc_final: 0.7535 (mp10) REVERT: A 442 PHE cc_start: 0.7700 (t80) cc_final: 0.7396 (t80) REVERT: A 454 ARG cc_start: 0.7349 (ttt180) cc_final: 0.6845 (ttm110) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.0610 time to fit residues: 6.3025 Evaluate side-chains 78 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 9 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 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 = 0.3909 r_free = 0.3909 target = 0.164874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129819 restraints weight = 4602.778| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.42 r_work: 0.3366 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3856 Z= 0.143 Angle : 0.539 6.496 5262 Z= 0.272 Chirality : 0.038 0.128 622 Planarity : 0.004 0.033 655 Dihedral : 4.807 59.629 536 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.04 % Allowed : 20.10 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.40), residues: 488 helix: 2.18 (0.28), residues: 365 sheet: -1.90 (1.32), residues: 10 loop : 0.87 (0.68), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.008 0.001 TYR A 354 PHE 0.015 0.001 PHE A 351 TRP 0.015 0.002 TRP A 346 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3854) covalent geometry : angle 0.53932 ( 5258) SS BOND : bond 0.00735 ( 2) SS BOND : angle 0.41830 ( 4) hydrogen bonds : bond 0.04420 ( 266) hydrogen bonds : angle 4.09188 ( 792) *********************** 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: 8 poor density : 76 time to evaluate : 0.140 Fit side-chains REVERT: A 46 THR cc_start: 0.8873 (m) cc_final: 0.8370 (p) REVERT: A 85 GLN cc_start: 0.8247 (mt0) cc_final: 0.7997 (mt0) REVERT: A 103 GLU cc_start: 0.7757 (pt0) cc_final: 0.7478 (pt0) REVERT: A 112 ASP cc_start: 0.8429 (t0) cc_final: 0.7994 (t0) REVERT: A 163 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7840 (mtmm) REVERT: A 316 GLU cc_start: 0.7556 (mp0) cc_final: 0.7079 (mp0) REVERT: A 417 GLN cc_start: 0.7875 (mp10) cc_final: 0.7533 (mp10) REVERT: A 442 PHE cc_start: 0.7707 (t80) cc_final: 0.7340 (t80) REVERT: A 454 ARG cc_start: 0.7485 (ttt180) cc_final: 0.6933 (ttm110) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.0619 time to fit residues: 6.4450 Evaluate side-chains 77 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.166842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132224 restraints weight = 4591.935| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.43 r_work: 0.3392 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4541 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= 0.125 Angle : 0.523 6.468 5262 Z= 0.265 Chirality : 0.037 0.120 622 Planarity : 0.004 0.034 655 Dihedral : 4.804 59.954 536 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.53 % Allowed : 21.12 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.40), residues: 488 helix: 2.24 (0.28), residues: 364 sheet: -1.61 (1.30), residues: 10 loop : 0.81 (0.69), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.007 0.001 TYR A 354 PHE 0.015 0.001 PHE A 351 TRP 0.019 0.002 TRP A 346 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3854) covalent geometry : angle 0.52326 ( 5258) SS BOND : bond 0.00647 ( 2) SS BOND : angle 0.46430 ( 4) hydrogen bonds : bond 0.04257 ( 266) hydrogen bonds : angle 4.02446 ( 792) *********************** 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 83 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.149 Fit side-chains REVERT: A 46 THR cc_start: 0.8864 (m) cc_final: 0.8343 (p) REVERT: A 85 GLN cc_start: 0.8334 (mt0) cc_final: 0.8124 (mt0) REVERT: A 103 GLU cc_start: 0.7725 (pt0) cc_final: 0.7471 (pt0) REVERT: A 112 ASP cc_start: 0.8332 (t0) cc_final: 0.7906 (t0) REVERT: A 212 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6744 (tt0) REVERT: A 316 GLU cc_start: 0.7603 (mp0) cc_final: 0.7112 (mp0) REVERT: A 417 GLN cc_start: 0.7893 (mp10) cc_final: 0.7549 (mp10) REVERT: A 442 PHE cc_start: 0.7690 (t80) cc_final: 0.7367 (t80) REVERT: A 454 ARG cc_start: 0.7434 (ttt180) cc_final: 0.7122 (ttm110) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.0666 time to fit residues: 6.7911 Evaluate side-chains 80 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3891 r_free = 0.3891 target = 0.162554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128381 restraints weight = 4472.933| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.43 r_work: 0.3383 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4652 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= 0.134 Angle : 0.533 6.319 5262 Z= 0.270 Chirality : 0.038 0.176 622 Planarity : 0.004 0.034 655 Dihedral : 4.744 59.523 536 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.78 % Allowed : 21.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.41), residues: 488 helix: 2.20 (0.28), residues: 365 sheet: -1.52 (1.34), residues: 10 loop : 0.85 (0.69), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 80 TYR 0.008 0.001 TYR A 354 PHE 0.015 0.001 PHE A 351 TRP 0.015 0.001 TRP A 346 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3854) covalent geometry : angle 0.53268 ( 5258) SS BOND : bond 0.00638 ( 2) SS BOND : angle 0.40096 ( 4) hydrogen bonds : bond 0.04253 ( 266) hydrogen bonds : angle 4.01560 ( 792) *********************** 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 84 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.142 Fit side-chains REVERT: A 46 THR cc_start: 0.8856 (m) cc_final: 0.8322 (p) REVERT: A 103 GLU cc_start: 0.7722 (pt0) cc_final: 0.7433 (pt0) REVERT: A 112 ASP cc_start: 0.8337 (t0) cc_final: 0.7912 (t0) REVERT: A 212 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6977 (mt-10) REVERT: A 316 GLU cc_start: 0.7598 (mp0) cc_final: 0.7101 (mp0) REVERT: A 417 GLN cc_start: 0.7947 (mp10) cc_final: 0.7601 (mp10) REVERT: A 442 PHE cc_start: 0.7723 (t80) cc_final: 0.7388 (t80) REVERT: A 454 ARG cc_start: 0.7464 (ttt180) cc_final: 0.7126 (ttm110) outliers start: 7 outliers final: 6 residues processed: 80 average time/residue: 0.0614 time to fit residues: 6.3401 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 : 0.144 ------------------------------------------------------------------------------- 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 377 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 438 PHE 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 26 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.0370 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 0.0570 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.167989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132352 restraints weight = 4629.504| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.57 r_work: 0.3429 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3856 Z= 0.119 Angle : 0.536 9.260 5262 Z= 0.266 Chirality : 0.037 0.163 622 Planarity : 0.004 0.034 655 Dihedral : 4.697 59.548 536 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.46 % Favored : 97.34 % Rotamer: Outliers : 2.04 % Allowed : 21.88 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.41), residues: 488 helix: 2.19 (0.28), residues: 366 sheet: -1.44 (1.36), residues: 10 loop : 0.88 (0.70), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 394 TYR 0.007 0.001 TYR A 264 PHE 0.015 0.001 PHE A 351 TRP 0.028 0.002 TRP A 346 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3854) covalent geometry : angle 0.53652 ( 5258) SS BOND : bond 0.00557 ( 2) SS BOND : angle 0.40510 ( 4) hydrogen bonds : bond 0.04074 ( 266) hydrogen bonds : angle 3.97546 ( 792) ********************** 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 83 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.167 Fit side-chains REVERT: A 46 THR cc_start: 0.8891 (m) cc_final: 0.8373 (p) REVERT: A 103 GLU cc_start: 0.7572 (pt0) cc_final: 0.7329 (pt0) REVERT: A 112 ASP cc_start: 0.8332 (t0) cc_final: 0.7936 (t0) REVERT: A 170 LEU cc_start: 0.8033 (tt) cc_final: 0.7717 (tp) REVERT: A 212 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6927 (tt0) REVERT: A 316 GLU cc_start: 0.7636 (mp0) cc_final: 0.7185 (mp0) REVERT: A 417 GLN cc_start: 0.7924 (mp10) cc_final: 0.7621 (mp10) REVERT: A 452 MET cc_start: 0.8405 (pmm) cc_final: 0.8128 (pmm) REVERT: A 454 ARG cc_start: 0.7470 (ttt180) cc_final: 0.7152 (ttm110) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.0621 time to fit residues: 6.4954 Evaluate side-chains 79 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 377 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 438 PHE 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 4 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.161637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127132 restraints weight = 4518.899| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.44 r_work: 0.3402 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4880 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= 0.145 Angle : 0.542 6.880 5262 Z= 0.272 Chirality : 0.038 0.151 622 Planarity : 0.004 0.034 655 Dihedral : 4.668 58.460 536 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.46 % Favored : 97.34 % Rotamer: Outliers : 1.78 % Allowed : 22.65 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.41), residues: 488 helix: 2.19 (0.28), residues: 365 sheet: -1.39 (1.39), residues: 10 loop : 0.82 (0.70), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 394 TYR 0.008 0.001 TYR A 354 PHE 0.027 0.002 PHE A 386 TRP 0.022 0.002 TRP A 346 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3854) covalent geometry : angle 0.54236 ( 5258) SS BOND : bond 0.00689 ( 2) SS BOND : angle 0.43284 ( 4) hydrogen bonds : bond 0.04240 ( 266) hydrogen bonds : angle 4.04353 ( 792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1016.53 seconds wall clock time: 18 minutes 11.60 seconds (1091.60 seconds total)