Starting phenix.real_space_refine on Wed Mar 12 06:15:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0l_15787/03_2025/8b0l_15787.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0l_15787/03_2025/8b0l_15787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b0l_15787/03_2025/8b0l_15787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0l_15787/03_2025/8b0l_15787.map" model { file = "/net/cci-nas-00/data/ceres_data/8b0l_15787/03_2025/8b0l_15787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0l_15787/03_2025/8b0l_15787.cif" } resolution = 3.13 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= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3861 atoms to isotropic. 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 14 5.16 5 C 2658 2.51 5 N 662 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4033 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3983 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 36, 'TRANS': 473} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.47, per 1000 atoms: 0.86 Number of scatterers: 4033 At special positions: 0 Unit cell: (60.298, 80.948, 85.904, 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 14 16.00 P 1 15.00 O 698 8.00 N 662 7.00 C 2658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 583.2 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 59.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.536A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 removed outlier: 3.609A pdb=" N PHE A 28 " --> pdb=" O THR A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 33 through 48 removed outlier: 4.018A pdb=" N ALA A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 70 Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.837A pdb=" N VAL A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 116 removed outlier: 4.195A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 126 through 142 removed outlier: 3.534A pdb=" N ALA A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 150 through 164 removed outlier: 4.329A pdb=" N ASP A 157 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 158 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 4.488A pdb=" N GLY A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 190 Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 204 through 209 removed outlier: 4.162A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.268A pdb=" N TRP A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 257 removed outlier: 4.198A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.922A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 412 through 416 removed outlier: 4.201A pdb=" N TRP A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 437 Processing helix chain 'A' and resid 481 through 487 Processing helix chain 'A' and resid 488 through 510 removed outlier: 3.704A pdb=" N ARG A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 227 Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 264 removed outlier: 6.935A pdb=" N ILE A 263 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 304 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.690A pdb=" N GLU A 381 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 408 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR A 383 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE A 410 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 385 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 407 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER A 443 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 409 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 451 " --> pdb=" O GLN A 459 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 579 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: 1.31 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 616 1.31 - 1.43: 1146 1.43 - 1.56: 2355 1.56 - 1.68: 3 1.68 - 1.81: 26 Bond restraints: 4146 Sorted by residual: bond pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.331 1.397 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CA PHE A 344 " pdb=" CB PHE A 344 " ideal model delta sigma weight residual 1.529 1.570 -0.041 1.54e-02 4.22e+03 7.15e+00 bond pdb=" C6 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.432 1.396 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.427 1.397 0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 4141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 5604 3.33 - 6.65: 46 6.65 - 9.98: 2 9.98 - 13.31: 1 13.31 - 16.63: 1 Bond angle restraints: 5654 Sorted by residual: angle pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O14 PTY A 601 " ideal model delta sigma weight residual 92.90 109.53 -16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O12 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O13 PTY A 601 " ideal model delta sigma weight residual 119.61 109.32 10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C11 PTY A 601 " pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 111.29 120.05 -8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" C31 PTY A 601 " pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 111.62 120.14 -8.52 3.00e+00 1.11e-01 8.07e+00 angle pdb=" N THR A 315 " pdb=" CA THR A 315 " pdb=" C THR A 315 " ideal model delta sigma weight residual 109.85 112.97 -3.12 1.58e+00 4.01e-01 3.89e+00 ... (remaining 5649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.06: 2341 20.06 - 40.13: 83 40.13 - 60.19: 12 60.19 - 80.25: 0 80.25 - 100.31: 4 Dihedral angle restraints: 2440 sinusoidal: 974 harmonic: 1466 Sorted by residual: dihedral pdb=" CA GLY A 71 " pdb=" C GLY A 71 " pdb=" N ILE A 72 " pdb=" CA ILE A 72 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual -59.77 40.54 -100.31 1 3.00e+01 1.11e-03 1.26e+01 dihedral pdb=" CA ASN A 314 " pdb=" C ASN A 314 " pdb=" N THR A 315 " pdb=" CA THR A 315 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 334 0.024 - 0.048: 168 0.048 - 0.072: 64 0.072 - 0.095: 44 0.095 - 0.119: 25 Chirality restraints: 635 Sorted by residual: chirality pdb=" CA ILE A 270 " pdb=" N ILE A 270 " pdb=" C ILE A 270 " pdb=" CB ILE A 270 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE A 231 " pdb=" N ILE A 231 " pdb=" C ILE A 231 " pdb=" CB ILE A 231 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 632 not shown) Planarity restraints: 708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 421 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 422 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 34 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 35 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 205 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.017 5.00e-02 4.00e+02 ... (remaining 705 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1000 2.80 - 3.32: 4009 3.32 - 3.85: 6877 3.85 - 4.37: 8068 4.37 - 4.90: 14214 Nonbonded interactions: 34168 Sorted by model distance: nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.270 3.040 nonbonded pdb=" O PHE A 151 " pdb=" OG SER A 154 " model vdw 2.278 3.040 nonbonded pdb=" O SER A 261 " pdb=" OG SER A 294 " model vdw 2.283 3.040 nonbonded pdb=" OD2 ASP A 331 " pdb=" OG SER A 376 " model vdw 2.297 3.040 nonbonded pdb=" ND2 ASN A 336 " pdb=" O GLY A 368 " model vdw 2.317 3.120 ... (remaining 34163 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.070 Find NCS groups from input model: 0.040 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4146 Z= 0.207 Angle : 0.665 16.632 5654 Z= 0.290 Chirality : 0.041 0.119 635 Planarity : 0.004 0.034 708 Dihedral : 10.816 100.314 1500 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.48 % Allowed : 3.12 % Favored : 96.39 % 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: 1.39 (0.41), residues: 508 helix: 2.21 (0.34), residues: 253 sheet: -0.26 (0.69), residues: 69 loop : -0.37 (0.51), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 492 HIS 0.001 0.001 HIS A 425 PHE 0.008 0.001 PHE A 174 TYR 0.008 0.001 TYR A 104 ARG 0.003 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.358 Fit side-chains REVERT: A 33 VAL cc_start: 0.8740 (t) cc_final: 0.8329 (p) REVERT: A 230 ASP cc_start: 0.8294 (t0) cc_final: 0.7954 (t0) REVERT: A 468 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7045 (tm-30) REVERT: A 488 ASN cc_start: 0.8490 (m-40) cc_final: 0.8288 (m110) outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.1531 time to fit residues: 17.4922 Evaluate side-chains 54 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.089861 restraints weight = 6400.223| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.85 r_work: 0.2871 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4146 Z= 0.209 Angle : 0.563 7.365 5654 Z= 0.277 Chirality : 0.043 0.134 635 Planarity : 0.005 0.040 708 Dihedral : 9.536 83.208 594 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.20 % Allowed : 8.17 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.40), residues: 508 helix: 2.03 (0.33), residues: 253 sheet: -0.68 (0.64), residues: 69 loop : -0.33 (0.51), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.001 HIS A 337 PHE 0.025 0.001 PHE A 465 TYR 0.014 0.001 TYR A 104 ARG 0.005 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.463 Fit side-chains REVERT: A 230 ASP cc_start: 0.8553 (t0) cc_final: 0.8297 (t0) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.1147 time to fit residues: 9.1767 Evaluate side-chains 53 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 444 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 37 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.117642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.090649 restraints weight = 6280.971| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.83 r_work: 0.2899 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4146 Z= 0.153 Angle : 0.528 5.525 5654 Z= 0.259 Chirality : 0.042 0.127 635 Planarity : 0.005 0.035 708 Dihedral : 8.874 89.959 594 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.44 % Allowed : 11.06 % Favored : 87.50 % 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: 1.24 (0.39), residues: 508 helix: 2.02 (0.33), residues: 259 sheet: -0.55 (0.62), residues: 69 loop : -0.33 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS A 337 PHE 0.018 0.001 PHE A 465 TYR 0.007 0.001 TYR A 388 ARG 0.005 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.448 Fit side-chains REVERT: A 33 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 230 ASP cc_start: 0.8324 (t0) cc_final: 0.7921 (t0) outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.1362 time to fit residues: 10.7699 Evaluate side-chains 55 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 444 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.0000 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.116471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089496 restraints weight = 6280.556| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.76 r_work: 0.2893 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4146 Z= 0.165 Angle : 0.520 5.258 5654 Z= 0.255 Chirality : 0.042 0.127 635 Planarity : 0.005 0.035 708 Dihedral : 8.139 80.584 594 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.92 % Allowed : 12.26 % Favored : 85.82 % 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: 1.26 (0.39), residues: 508 helix: 2.03 (0.33), residues: 259 sheet: -0.46 (0.61), residues: 69 loop : -0.33 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS A 337 PHE 0.016 0.001 PHE A 465 TYR 0.009 0.001 TYR A 388 ARG 0.003 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.416 Fit side-chains REVERT: A 33 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 230 ASP cc_start: 0.8254 (t0) cc_final: 0.7867 (t0) REVERT: A 343 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8222 (mt-10) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.1086 time to fit residues: 8.8244 Evaluate side-chains 56 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 257 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.089370 restraints weight = 6508.801| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.83 r_work: 0.2886 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4146 Z= 0.162 Angle : 0.513 5.237 5654 Z= 0.251 Chirality : 0.042 0.125 635 Planarity : 0.005 0.042 708 Dihedral : 7.353 65.948 594 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.16 % Allowed : 11.30 % Favored : 86.54 % 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: 1.36 (0.39), residues: 508 helix: 2.07 (0.33), residues: 258 sheet: -0.30 (0.61), residues: 69 loop : -0.25 (0.50), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 132 HIS 0.001 0.000 HIS A 337 PHE 0.011 0.001 PHE A 465 TYR 0.012 0.001 TYR A 104 ARG 0.003 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.424 Fit side-chains REVERT: A 33 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 230 ASP cc_start: 0.8250 (t0) cc_final: 0.7869 (t0) REVERT: A 285 ASP cc_start: 0.8900 (t70) cc_final: 0.8528 (t0) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 0.1165 time to fit residues: 10.0857 Evaluate side-chains 57 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.089321 restraints weight = 6319.057| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.78 r_work: 0.2868 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4146 Z= 0.208 Angle : 0.530 5.301 5654 Z= 0.260 Chirality : 0.043 0.125 635 Planarity : 0.005 0.038 708 Dihedral : 6.973 55.500 594 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.16 % Allowed : 11.54 % Favored : 86.30 % 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: 1.36 (0.39), residues: 508 helix: 2.06 (0.33), residues: 257 sheet: -0.26 (0.61), residues: 69 loop : -0.24 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS A 337 PHE 0.011 0.001 PHE A 465 TYR 0.011 0.001 TYR A 104 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.452 Fit side-chains REVERT: A 230 ASP cc_start: 0.8330 (t0) cc_final: 0.7920 (t0) REVERT: A 285 ASP cc_start: 0.8882 (t70) cc_final: 0.8344 (t0) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.1099 time to fit residues: 9.1171 Evaluate side-chains 57 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 257 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.116231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.088753 restraints weight = 6374.487| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.87 r_work: 0.2870 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4146 Z= 0.188 Angle : 0.539 7.149 5654 Z= 0.262 Chirality : 0.043 0.126 635 Planarity : 0.005 0.040 708 Dihedral : 6.744 53.912 594 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.68 % Allowed : 12.74 % Favored : 85.58 % 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: 1.27 (0.39), residues: 508 helix: 2.06 (0.33), residues: 257 sheet: -0.42 (0.64), residues: 59 loop : -0.38 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.000 0.000 HIS A 337 PHE 0.011 0.001 PHE A 465 TYR 0.013 0.001 TYR A 104 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.400 Fit side-chains REVERT: A 230 ASP cc_start: 0.8245 (t0) cc_final: 0.7854 (t0) REVERT: A 285 ASP cc_start: 0.8908 (t70) cc_final: 0.8496 (t0) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.1052 time to fit residues: 8.8951 Evaluate side-chains 59 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 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 = 0.3393 r_free = 0.3393 target = 0.116696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.089323 restraints weight = 6272.468| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.84 r_work: 0.2878 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4146 Z= 0.167 Angle : 0.525 5.307 5654 Z= 0.259 Chirality : 0.042 0.130 635 Planarity : 0.005 0.037 708 Dihedral : 6.557 52.657 594 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.92 % Allowed : 12.50 % Favored : 85.58 % 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: 1.35 (0.39), residues: 508 helix: 2.08 (0.33), residues: 257 sheet: -0.27 (0.62), residues: 69 loop : -0.30 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.001 0.001 HIS A 337 PHE 0.008 0.001 PHE A 82 TYR 0.013 0.001 TYR A 104 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.479 Fit side-chains REVERT: A 230 ASP cc_start: 0.8238 (t0) cc_final: 0.7857 (t0) REVERT: A 285 ASP cc_start: 0.8888 (t70) cc_final: 0.8465 (t0) REVERT: A 341 PHE cc_start: 0.8829 (m-10) cc_final: 0.8560 (m-10) REVERT: A 411 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.9057 (p) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.1104 time to fit residues: 9.3382 Evaluate side-chains 56 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 411 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 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 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090972 restraints weight = 6322.084| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.80 r_work: 0.2896 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4146 Z= 0.163 Angle : 0.525 5.206 5654 Z= 0.258 Chirality : 0.042 0.127 635 Planarity : 0.005 0.039 708 Dihedral : 6.402 49.974 594 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.68 % Allowed : 13.22 % Favored : 85.10 % 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: 1.22 (0.39), residues: 508 helix: 2.05 (0.33), residues: 258 sheet: -0.37 (0.65), residues: 59 loop : -0.49 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 74 HIS 0.001 0.001 HIS A 337 PHE 0.007 0.001 PHE A 174 TYR 0.012 0.001 TYR A 104 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.456 Fit side-chains REVERT: A 230 ASP cc_start: 0.8233 (t0) cc_final: 0.7868 (t0) REVERT: A 285 ASP cc_start: 0.8883 (t70) cc_final: 0.8308 (t0) REVERT: A 341 PHE cc_start: 0.8841 (m-10) cc_final: 0.8583 (m-10) REVERT: A 411 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.9041 (p) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.1093 time to fit residues: 8.6966 Evaluate side-chains 57 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 411 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088985 restraints weight = 6346.455| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.86 r_work: 0.2875 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4146 Z= 0.193 Angle : 0.541 9.422 5654 Z= 0.259 Chirality : 0.043 0.129 635 Planarity : 0.005 0.034 708 Dihedral : 6.404 49.824 594 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.92 % Allowed : 13.22 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.39), residues: 508 helix: 2.04 (0.33), residues: 258 sheet: -0.43 (0.66), residues: 59 loop : -0.50 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 74 HIS 0.002 0.001 HIS A 337 PHE 0.007 0.001 PHE A 174 TYR 0.012 0.001 TYR A 104 ARG 0.002 0.000 ARG A 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.427 Fit side-chains REVERT: A 230 ASP cc_start: 0.8254 (t0) cc_final: 0.7875 (t0) REVERT: A 285 ASP cc_start: 0.8895 (t70) cc_final: 0.8328 (t0) REVERT: A 341 PHE cc_start: 0.8836 (m-10) cc_final: 0.8578 (m-10) REVERT: A 411 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.9033 (p) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.1059 time to fit residues: 8.4416 Evaluate side-chains 56 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 411 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.0170 chunk 27 optimal weight: 0.0010 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 overall best weight: 0.4224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.090858 restraints weight = 6255.064| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.81 r_work: 0.2910 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4146 Z= 0.145 Angle : 0.524 5.959 5654 Z= 0.257 Chirality : 0.042 0.129 635 Planarity : 0.005 0.041 708 Dihedral : 6.290 48.367 594 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.44 % Allowed : 13.46 % Favored : 85.10 % 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: 1.30 (0.39), residues: 508 helix: 2.09 (0.33), residues: 258 sheet: -0.31 (0.63), residues: 69 loop : -0.41 (0.50), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.001 0.001 HIS A 337 PHE 0.011 0.001 PHE A 416 TYR 0.013 0.001 TYR A 104 ARG 0.002 0.000 ARG A 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1988.37 seconds wall clock time: 35 minutes 0.38 seconds (2100.38 seconds total)