Starting phenix.real_space_refine on Tue Feb 11 05:57:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtv_37843/02_2025/8wtv_37843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtv_37843/02_2025/8wtv_37843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtv_37843/02_2025/8wtv_37843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtv_37843/02_2025/8wtv_37843.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtv_37843/02_2025/8wtv_37843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtv_37843/02_2025/8wtv_37843.cif" } resolution = 2.7 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= 0.067 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: 6 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2897 2.51 5 N 667 2.21 5 O 738 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-5592/modules/chem_data/mon_lib" Total number of atoms: 4325 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4281 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 516} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 44 Unusual residues: {' CL': 1, ' NA': 2, 'E5E': 2, 'NAG': 1} Classifications: {'undetermined': 6, 'water': 3} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.07, per 1000 atoms: 0.71 Number of scatterers: 4325 At special positions: 0 Unit cell: (77.35, 67.15, 90.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 20 16.00 Na 2 11.00 O 738 8.00 N 667 7.00 C 2897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.02 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 Links applied NAG-ASN " NAG A 706 " - " ASN A 184 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 964.9 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 79.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 76 through 89 removed outlier: 4.670A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.504A pdb=" N TYR A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.551A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.662A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 129 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 135 through 166 removed outlier: 3.788A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.639A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.620A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.761A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.362A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.732A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.525A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.868A pdb=" N THR A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.876A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 497 through 510 removed outlier: 3.557A pdb=" N MET A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.688A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 583 through 593 removed outlier: 3.577A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.944A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.856A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.076A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 265 hydrogen bonds defined for protein. 771 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: 1.02 Time building geometry restraints manager: 1.32 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: 635 1.31 - 1.43: 1405 1.43 - 1.56: 2387 1.56 - 1.68: 1 1.68 - 1.81: 31 Bond restraints: 4459 Sorted by residual: bond pdb=" CA MET A 107 " pdb=" C MET A 107 " ideal model delta sigma weight residual 1.520 1.572 -0.052 1.23e-02 6.61e+03 1.80e+01 bond pdb=" C LYS A 576 " pdb=" O LYS A 576 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.26e-02 6.30e+03 1.70e+01 bond pdb=" C LYS A 576 " pdb=" N PHE A 577 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.36e-02 5.41e+03 1.19e+01 bond pdb=" C MET A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.36e-02 5.41e+03 1.17e+01 bond pdb=" C SER A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 1.337 1.370 -0.033 9.80e-03 1.04e+04 1.14e+01 ... (remaining 4454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 5906 1.31 - 2.61: 139 2.61 - 3.92: 25 3.92 - 5.23: 11 5.23 - 6.53: 5 Bond angle restraints: 6086 Sorted by residual: angle pdb=" N TRP A 253 " pdb=" CA TRP A 253 " pdb=" C TRP A 253 " ideal model delta sigma weight residual 113.01 118.40 -5.39 1.20e+00 6.94e-01 2.02e+01 angle pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 117.48 122.12 -4.64 1.15e+00 7.56e-01 1.63e+01 angle pdb=" O SER A 182 " pdb=" C SER A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 121.53 117.15 4.38 1.12e+00 7.97e-01 1.53e+01 angle pdb=" N ASN A 184 " pdb=" CA ASN A 184 " pdb=" C ASN A 184 " ideal model delta sigma weight residual 113.38 108.98 4.40 1.23e+00 6.61e-01 1.28e+01 angle pdb=" O TYR A 575 " pdb=" C TYR A 575 " pdb=" N LYS A 576 " ideal model delta sigma weight residual 122.12 118.36 3.76 1.06e+00 8.90e-01 1.26e+01 ... (remaining 6081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2187 17.99 - 35.97: 236 35.97 - 53.96: 63 53.96 - 71.95: 12 71.95 - 89.94: 2 Dihedral angle restraints: 2500 sinusoidal: 951 harmonic: 1549 Sorted by residual: dihedral pdb=" CB CYS A 176 " pdb=" SG CYS A 176 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -175.94 89.94 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CG ARG A 442 " pdb=" CD ARG A 442 " pdb=" NE ARG A 442 " pdb=" CZ ARG A 442 " ideal model delta sinusoidal sigma weight residual 90.00 132.55 -42.55 2 1.50e+01 4.44e-03 9.76e+00 dihedral pdb=" CA LYS A 576 " pdb=" CB LYS A 576 " pdb=" CG LYS A 576 " pdb=" CD LYS A 576 " ideal model delta sinusoidal sigma weight residual 180.00 120.06 59.94 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 504 0.045 - 0.090: 148 0.090 - 0.134: 25 0.134 - 0.179: 0 0.179 - 0.224: 4 Chirality restraints: 681 Sorted by residual: chirality pdb=" C1 NAG A 706 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 706 " pdb=" O5 NAG A 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA TRP A 253 " pdb=" N TRP A 253 " pdb=" C TRP A 253 " pdb=" CB TRP A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CAL E5E A 704 " pdb=" CAH E5E A 704 " pdb=" CAK E5E A 704 " pdb=" OAD E5E A 704 " both_signs ideal model delta sigma weight residual False -2.31 -2.51 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 678 not shown) Planarity restraints: 739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 706 " 0.248 2.00e-02 2.50e+03 2.09e-01 5.45e+02 pdb=" C7 NAG A 706 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A 706 " 0.170 2.00e-02 2.50e+03 pdb=" N2 NAG A 706 " -0.351 2.00e-02 2.50e+03 pdb=" O7 NAG A 706 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 106 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C GLY A 106 " 0.029 2.00e-02 2.50e+03 pdb=" O GLY A 106 " -0.011 2.00e-02 2.50e+03 pdb=" N MET A 107 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 82 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 83 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.021 5.00e-02 4.00e+02 ... (remaining 736 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1259 2.82 - 3.34: 3885 3.34 - 3.86: 7037 3.86 - 4.38: 8265 4.38 - 4.90: 14400 Nonbonded interactions: 34846 Sorted by model distance: nonbonded pdb=" OD1 ASN A 350 " pdb="NA NA A 701 " model vdw 2.297 2.470 nonbonded pdb=" O ALA A 394 " pdb=" OG1 THR A 397 " model vdw 2.299 3.040 nonbonded pdb=" O SER A 259 " pdb=" OG SER A 259 " model vdw 2.319 3.040 nonbonded pdb=" NH2 ARG A 341 " pdb=" OD1 ASP A 342 " model vdw 2.319 3.120 nonbonded pdb=" O ARG A 442 " pdb=" OG1 THR A 446 " model vdw 2.346 3.040 ... (remaining 34841 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4459 Z= 0.228 Angle : 0.545 6.532 6086 Z= 0.310 Chirality : 0.043 0.224 681 Planarity : 0.009 0.209 738 Dihedral : 15.806 81.789 1511 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.22 % Allowed : 16.41 % Favored : 83.37 % 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: 1.82 (0.38), residues: 532 helix: 1.99 (0.29), residues: 358 sheet: None (None), residues: 0 loop : -0.41 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 553 HIS 0.002 0.000 HIS A 599 PHE 0.010 0.001 PHE A 409 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.496 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 1.1250 time to fit residues: 54.2701 Evaluate side-chains 45 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3057 r_free = 0.3057 target = 0.105606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.091903 restraints weight = 4697.722| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 0.95 r_work: 0.2765 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4459 Z= 0.246 Angle : 0.567 5.571 6086 Z= 0.307 Chirality : 0.043 0.150 681 Planarity : 0.005 0.037 738 Dihedral : 6.823 53.794 614 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.66 % Allowed : 14.41 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.38), residues: 532 helix: 1.84 (0.28), residues: 361 sheet: None (None), residues: 0 loop : -0.53 (0.48), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 553 HIS 0.003 0.001 HIS A 222 PHE 0.017 0.002 PHE A 409 TYR 0.021 0.002 TYR A 84 ARG 0.005 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.448 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 50 average time/residue: 1.0521 time to fit residues: 55.0688 Evaluate side-chains 46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.108984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.094554 restraints weight = 4650.748| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.04 r_work: 0.2818 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4459 Z= 0.159 Angle : 0.483 5.412 6086 Z= 0.262 Chirality : 0.039 0.132 681 Planarity : 0.004 0.036 738 Dihedral : 5.538 45.696 610 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.77 % Allowed : 15.30 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.38), residues: 532 helix: 2.09 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.51 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 553 HIS 0.002 0.000 HIS A 222 PHE 0.010 0.001 PHE A 409 TYR 0.019 0.001 TYR A 84 ARG 0.005 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.477 Fit side-chains REVERT: A 256 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7479 (m) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 1.1077 time to fit residues: 54.4755 Evaluate side-chains 48 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 0.0370 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.109137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.094035 restraints weight = 4740.451| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.14 r_work: 0.2811 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4459 Z= 0.154 Angle : 0.473 5.466 6086 Z= 0.256 Chirality : 0.039 0.130 681 Planarity : 0.004 0.035 738 Dihedral : 5.259 39.664 610 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.00 % Allowed : 15.52 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.38), residues: 532 helix: 2.16 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.45 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 553 HIS 0.001 0.000 HIS A 222 PHE 0.010 0.001 PHE A 409 TYR 0.018 0.001 TYR A 84 ARG 0.006 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.439 Fit side-chains REVERT: A 256 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7465 (m) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 1.0888 time to fit residues: 58.1297 Evaluate side-chains 49 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3124 r_free = 0.3124 target = 0.110521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.095622 restraints weight = 4780.398| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.11 r_work: 0.2839 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4459 Z= 0.143 Angle : 0.457 5.401 6086 Z= 0.247 Chirality : 0.039 0.126 681 Planarity : 0.004 0.034 738 Dihedral : 4.973 33.182 610 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.55 % Allowed : 15.96 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.38), residues: 532 helix: 2.24 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.39 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 553 HIS 0.001 0.000 HIS A 222 PHE 0.008 0.001 PHE A 409 TYR 0.017 0.001 TYR A 84 ARG 0.006 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.453 Fit side-chains REVERT: A 256 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7445 (m) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 1.0442 time to fit residues: 54.8398 Evaluate side-chains 50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.110416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.095973 restraints weight = 4658.499| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.05 r_work: 0.2833 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4459 Z= 0.151 Angle : 0.467 5.514 6086 Z= 0.252 Chirality : 0.039 0.129 681 Planarity : 0.004 0.033 738 Dihedral : 4.948 30.585 610 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.33 % Allowed : 16.41 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.38), residues: 532 helix: 2.23 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.35 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 553 HIS 0.002 0.000 HIS A 222 PHE 0.010 0.001 PHE A 409 TYR 0.018 0.001 TYR A 84 ARG 0.006 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.583 Fit side-chains REVERT: A 256 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7468 (m) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 1.0431 time to fit residues: 53.6580 Evaluate side-chains 51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.0070 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.111284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.098509 restraints weight = 4651.498| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 0.97 r_work: 0.2854 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4459 Z= 0.155 Angle : 0.471 5.585 6086 Z= 0.255 Chirality : 0.039 0.131 681 Planarity : 0.004 0.034 738 Dihedral : 4.934 30.895 610 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.00 % Allowed : 15.74 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.38), residues: 532 helix: 2.21 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.36 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 553 HIS 0.002 0.000 HIS A 222 PHE 0.010 0.001 PHE A 409 TYR 0.018 0.001 TYR A 84 ARG 0.007 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.503 Fit side-chains REVERT: A 256 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7577 (m) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 1.0644 time to fit residues: 56.8927 Evaluate side-chains 52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3069 r_free = 0.3069 target = 0.106663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.091435 restraints weight = 4649.783| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.11 r_work: 0.2767 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4459 Z= 0.220 Angle : 0.538 5.948 6086 Z= 0.290 Chirality : 0.042 0.148 681 Planarity : 0.005 0.036 738 Dihedral : 5.396 33.933 610 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.77 % Allowed : 16.41 % Favored : 81.82 % 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: 1.85 (0.38), residues: 532 helix: 1.98 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.44 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 585 HIS 0.003 0.001 HIS A 222 PHE 0.016 0.002 PHE A 409 TYR 0.020 0.002 TYR A 84 ARG 0.007 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.482 Fit side-chains REVERT: A 256 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7442 (m) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 1.1853 time to fit residues: 57.1200 Evaluate side-chains 49 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.0170 chunk 37 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 overall best weight: 1.0220 ------------------------------------------------------------------------------- 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 = 0.3120 r_free = 0.3120 target = 0.109920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.097770 restraints weight = 4676.051| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 0.88 r_work: 0.2830 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4459 Z= 0.186 Angle : 0.506 5.776 6086 Z= 0.274 Chirality : 0.040 0.139 681 Planarity : 0.004 0.035 738 Dihedral : 5.213 32.893 610 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.55 % Allowed : 16.85 % Favored : 81.60 % 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: 1.94 (0.38), residues: 532 helix: 2.06 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.44 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 585 HIS 0.002 0.001 HIS A 222 PHE 0.013 0.001 PHE A 409 TYR 0.019 0.001 TYR A 84 ARG 0.007 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.448 Fit side-chains REVERT: A 256 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7599 (m) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 1.1530 time to fit residues: 54.3236 Evaluate side-chains 48 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.109324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.095755 restraints weight = 4608.279| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 0.94 r_work: 0.2825 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4459 Z= 0.166 Angle : 0.484 5.599 6086 Z= 0.262 Chirality : 0.040 0.134 681 Planarity : 0.004 0.034 738 Dihedral : 5.015 31.839 610 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.77 % Allowed : 16.41 % Favored : 81.82 % 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: 2.05 (0.38), residues: 532 helix: 2.14 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.39 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 585 HIS 0.002 0.000 HIS A 222 PHE 0.011 0.001 PHE A 409 TYR 0.019 0.001 TYR A 84 ARG 0.007 0.000 ARG A 604 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.432 Fit side-chains REVERT: A 256 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7558 (m) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 1.0971 time to fit residues: 56.2578 Evaluate side-chains 51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 375 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3118 r_free = 0.3118 target = 0.109879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.097166 restraints weight = 4649.942| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 0.96 r_work: 0.2829 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4459 Z= 0.173 Angle : 0.493 5.728 6086 Z= 0.267 Chirality : 0.040 0.135 681 Planarity : 0.004 0.034 738 Dihedral : 5.033 32.068 610 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.00 % Allowed : 16.19 % Favored : 81.82 % 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: 2.01 (0.38), residues: 532 helix: 2.11 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.40 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 585 HIS 0.002 0.000 HIS A 222 PHE 0.012 0.001 PHE A 409 TYR 0.019 0.001 TYR A 84 ARG 0.007 0.000 ARG A 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2887.06 seconds wall clock time: 51 minutes 59.62 seconds (3119.62 seconds total)