Starting phenix.real_space_refine on Fri Jan 17 14:37:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjx_38409/01_2025/8xjx_38409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjx_38409/01_2025/8xjx_38409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjx_38409/01_2025/8xjx_38409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjx_38409/01_2025/8xjx_38409.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjx_38409/01_2025/8xjx_38409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjx_38409/01_2025/8xjx_38409.cif" } resolution = 2.78 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= 0.000 sd= 0.073 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 5737 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 32 5.49 5 S 29 5.16 5 C 3914 2.51 5 N 1120 2.21 5 O 1215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6311 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5626 Classifications: {'peptide': 693} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 23, 'TRANS': 669} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 298 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1, 'water': 18} Link IDs: {None: 18} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 4.46, per 1000 atoms: 0.71 Number of scatterers: 6311 At special positions: 0 Unit cell: (75.739, 91.908, 107.226, 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) Mn 1 24.99 S 29 16.00 P 32 15.00 O 1215 8.00 N 1120 7.00 C 3914 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: 1.46 Conformation dependent library (CDL) restraints added in 916.2 milliseconds 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 7 sheets defined 36.9% alpha, 18.5% beta 11 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 84 through 108 removed outlier: 3.686A pdb=" N HIS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.856A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.544A pdb=" N LEU A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 removed outlier: 3.606A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 445 removed outlier: 3.601A pdb=" N GLY A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.643A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.514A pdb=" N LYS A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.974A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 613 removed outlier: 3.649A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.530A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.644A pdb=" N ALA A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 4.891A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.637A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS A 522 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N HIS A 594 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 382 removed outlier: 9.119A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1650 1.33 - 1.45: 1324 1.45 - 1.57: 3404 1.57 - 1.69: 63 1.69 - 1.81: 51 Bond restraints: 6492 Sorted by residual: bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.599 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" N VAL A 606 " pdb=" CA VAL A 606 " ideal model delta sigma weight residual 1.461 1.502 -0.041 1.17e-02 7.31e+03 1.21e+01 bond pdb=" N GLU A 607 " pdb=" CA GLU A 607 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.23e-02 6.61e+03 3.37e+00 bond pdb=" CA GLU A 607 " pdb=" C GLU A 607 " ideal model delta sigma weight residual 1.524 1.539 -0.016 1.29e-02 6.01e+03 1.45e+00 bond pdb=" C GLU A 607 " pdb=" O GLU A 607 " ideal model delta sigma weight residual 1.237 1.223 0.013 1.19e-02 7.06e+03 1.27e+00 ... (remaining 6487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 8715 1.72 - 3.43: 167 3.43 - 5.15: 28 5.15 - 6.87: 4 6.87 - 8.58: 3 Bond angle restraints: 8917 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.33 110.58 -7.25 9.30e-01 1.16e+00 6.07e+01 angle pdb=" C GLU A 607 " pdb=" CA GLU A 607 " pdb=" CB GLU A 607 " ideal model delta sigma weight residual 110.85 119.43 -8.58 1.70e+00 3.46e-01 2.55e+01 angle pdb=" N VAL A 606 " pdb=" CA VAL A 606 " pdb=" CB VAL A 606 " ideal model delta sigma weight residual 110.55 115.67 -5.12 1.17e+00 7.31e-01 1.92e+01 angle pdb=" C GLU A 607 " pdb=" N LYS A 608 " pdb=" CA LYS A 608 " ideal model delta sigma weight residual 120.38 115.29 5.09 1.37e+00 5.33e-01 1.38e+01 angle pdb=" C GLY A 167 " pdb=" N LYS A 168 " pdb=" CA LYS A 168 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 ... (remaining 8912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.50: 3529 26.50 - 53.00: 240 53.00 - 79.51: 25 79.51 - 106.01: 1 106.01 - 132.51: 1 Dihedral angle restraints: 3796 sinusoidal: 1751 harmonic: 2045 Sorted by residual: dihedral pdb=" CA MET A 610 " pdb=" C MET A 610 " pdb=" N SER A 611 " pdb=" CA SER A 611 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLY A 547 " pdb=" C GLY A 547 " pdb=" N HIS A 548 " pdb=" CA HIS A 548 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 87.49 132.51 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 3793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 876 0.064 - 0.127: 108 0.127 - 0.191: 8 0.191 - 0.254: 1 0.254 - 0.318: 2 Chirality restraints: 995 Sorted by residual: chirality pdb=" P DT B 1 " pdb=" OP1 DT B 1 " pdb=" OP2 DT B 1 " pdb=" O5' DT B 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.66 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL A 606 " pdb=" CA VAL A 606 " pdb=" CG1 VAL A 606 " pdb=" CG2 VAL A 606 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO A 474 " pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CB PRO A 474 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 992 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 125 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C ARG A 125 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG A 125 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 126 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 43 " 0.012 2.00e-02 2.50e+03 8.90e-03 1.98e+00 pdb=" CG TRP A 43 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 43 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 43 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 43 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 43 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 43 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 43 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 43 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 43 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO A 511 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " 0.019 5.00e-02 4.00e+02 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 12 2.37 - 3.00: 3106 3.00 - 3.64: 9087 3.64 - 4.27: 14789 4.27 - 4.90: 24417 Nonbonded interactions: 51411 Sorted by model distance: nonbonded pdb=" OXT VAL A 737 " pdb="MN MN A 801 " model vdw 1.742 2.320 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN A 801 " model vdw 1.797 2.320 nonbonded pdb=" O SER A 313 " pdb=" O HOH A 901 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 668 " pdb=" O HOH A 902 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 265 " pdb=" O HOH A 903 " model vdw 2.263 3.040 ... (remaining 51406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 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 0.119 6492 Z= 0.213 Angle : 0.601 8.585 8917 Z= 0.352 Chirality : 0.044 0.318 995 Planarity : 0.004 0.035 1020 Dihedral : 16.486 132.512 2474 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.51 % Favored : 95.20 % Rotamer: Outliers : 0.16 % Allowed : 0.49 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.31), residues: 687 helix: 0.76 (0.33), residues: 240 sheet: 1.12 (0.43), residues: 130 loop : -1.47 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 43 HIS 0.003 0.001 HIS A 710 PHE 0.017 0.001 PHE A 351 TYR 0.009 0.001 TYR A 53 ARG 0.004 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.629 Fit side-chains REVERT: A 400 HIS cc_start: 0.7151 (m90) cc_final: 0.6834 (m90) outliers start: 1 outliers final: 2 residues processed: 112 average time/residue: 1.2185 time to fit residues: 143.3115 Evaluate side-chains 76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 575 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.0670 chunk 18 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 376 GLN A 435 GLN A 552 GLN A 583 GLN A 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.203009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.186757 restraints weight = 5705.342| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 1.21 r_work: 0.3781 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6492 Z= 0.216 Angle : 0.578 5.825 8917 Z= 0.325 Chirality : 0.042 0.155 995 Planarity : 0.004 0.049 1020 Dihedral : 16.386 136.191 1117 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.68 % Favored : 94.03 % Rotamer: Outliers : 2.63 % Allowed : 12.01 % Favored : 85.36 % 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: -0.16 (0.31), residues: 687 helix: 0.87 (0.33), residues: 253 sheet: 0.96 (0.42), residues: 122 loop : -1.41 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 PHE 0.015 0.002 PHE A 351 TYR 0.008 0.001 TYR A 690 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.625 Fit side-chains REVERT: A 111 ARG cc_start: 0.7886 (ptm160) cc_final: 0.7641 (mtp-110) REVERT: A 122 GLN cc_start: 0.6022 (tt0) cc_final: 0.5752 (mt0) REVERT: A 400 HIS cc_start: 0.7410 (m90) cc_final: 0.7132 (m90) REVERT: A 414 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7680 (mp10) REVERT: A 464 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6610 (mp) REVERT: A 532 ASN cc_start: 0.7636 (m-40) cc_final: 0.7375 (m-40) REVERT: A 667 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7472 (ttt) outliers start: 16 outliers final: 3 residues processed: 82 average time/residue: 1.1764 time to fit residues: 101.9164 Evaluate side-chains 68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 724 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 27 optimal weight: 0.0370 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 152 HIS A 370 GLN A 510 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 627 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.194170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.176980 restraints weight = 5733.122| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.28 r_work: 0.3665 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 6492 Z= 0.496 Angle : 0.788 9.513 8917 Z= 0.430 Chirality : 0.050 0.188 995 Planarity : 0.006 0.069 1020 Dihedral : 17.101 142.761 1114 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.42 % Favored : 92.43 % Rotamer: Outliers : 5.43 % Allowed : 12.34 % Favored : 82.24 % 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: -0.82 (0.30), residues: 687 helix: 0.16 (0.31), residues: 253 sheet: 1.03 (0.44), residues: 102 loop : -1.65 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 43 HIS 0.006 0.001 HIS A 320 PHE 0.024 0.003 PHE A 101 TYR 0.015 0.003 TYR A 440 ARG 0.008 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.641 Fit side-chains REVERT: A 59 MET cc_start: 0.8292 (ttm) cc_final: 0.8041 (ttm) REVERT: A 126 GLN cc_start: 0.7459 (tt0) cc_final: 0.6868 (tm-30) REVERT: A 464 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6624 (mp) REVERT: A 532 ASN cc_start: 0.7917 (m-40) cc_final: 0.7620 (m-40) outliers start: 33 outliers final: 11 residues processed: 95 average time/residue: 1.1711 time to fit residues: 117.3106 Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 724 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 400 HIS A 435 GLN A 541 ASN A 575 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.202223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.179244 restraints weight = 5844.986| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.48 r_work: 0.3804 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6492 Z= 0.175 Angle : 0.560 7.935 8917 Z= 0.313 Chirality : 0.041 0.147 995 Planarity : 0.004 0.047 1020 Dihedral : 16.184 125.951 1114 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 3.78 % Allowed : 16.45 % Favored : 79.77 % 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: -0.27 (0.31), residues: 687 helix: 0.70 (0.33), residues: 258 sheet: 1.03 (0.43), residues: 122 loop : -1.48 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 43 HIS 0.004 0.001 HIS A 590 PHE 0.020 0.001 PHE A 351 TYR 0.009 0.001 TYR A 617 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.781 Fit side-chains REVERT: A 82 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7079 (mp) REVERT: A 126 GLN cc_start: 0.7141 (tt0) cc_final: 0.6847 (tm-30) REVERT: A 128 ILE cc_start: 0.6340 (OUTLIER) cc_final: 0.6065 (mt) REVERT: A 414 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7608 (mp10) REVERT: A 464 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7130 (mp) outliers start: 23 outliers final: 8 residues processed: 77 average time/residue: 1.0221 time to fit residues: 84.2344 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 510 GLN A 541 ASN A 575 GLN A 638 ASN A 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.200689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.176531 restraints weight = 5783.292| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.54 r_work: 0.3714 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6492 Z= 0.208 Angle : 0.575 8.469 8917 Z= 0.320 Chirality : 0.042 0.157 995 Planarity : 0.004 0.048 1020 Dihedral : 16.238 129.151 1111 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.40 % Favored : 93.45 % Rotamer: Outliers : 4.28 % Allowed : 17.76 % Favored : 77.96 % 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: -0.17 (0.31), residues: 687 helix: 0.81 (0.33), residues: 253 sheet: 0.98 (0.43), residues: 125 loop : -1.40 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 43 HIS 0.003 0.001 HIS A 590 PHE 0.016 0.002 PHE A 351 TYR 0.009 0.001 TYR A 20 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.626 Fit side-chains REVERT: A 82 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7054 (mp) REVERT: A 126 GLN cc_start: 0.7357 (tt0) cc_final: 0.6634 (tm-30) REVERT: A 128 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.6183 (mt) REVERT: A 155 GLU cc_start: 0.6425 (tp30) cc_final: 0.6060 (tt0) REVERT: A 464 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6651 (mp) outliers start: 26 outliers final: 11 residues processed: 77 average time/residue: 0.9191 time to fit residues: 75.8070 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 510 GLN A 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.196002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.172104 restraints weight = 5785.043| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.50 r_work: 0.3648 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 6492 Z= 0.422 Angle : 0.724 9.676 8917 Z= 0.397 Chirality : 0.048 0.190 995 Planarity : 0.005 0.062 1020 Dihedral : 16.869 139.303 1111 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.13 % Favored : 92.72 % Rotamer: Outliers : 4.44 % Allowed : 18.09 % Favored : 77.47 % 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: -0.74 (0.30), residues: 687 helix: 0.25 (0.32), residues: 254 sheet: 1.06 (0.46), residues: 102 loop : -1.63 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 43 HIS 0.005 0.001 HIS A 320 PHE 0.020 0.003 PHE A 101 TYR 0.014 0.002 TYR A 440 ARG 0.006 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.647 Fit side-chains REVERT: A 82 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7199 (mp) REVERT: A 123 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: A 126 GLN cc_start: 0.7461 (tt0) cc_final: 0.6681 (tm-30) REVERT: A 128 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6214 (mt) REVERT: A 155 GLU cc_start: 0.6599 (tp30) cc_final: 0.6233 (tt0) REVERT: A 464 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6670 (mp) REVERT: A 721 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7802 (mtt-85) outliers start: 27 outliers final: 13 residues processed: 81 average time/residue: 1.1305 time to fit residues: 96.7923 Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 400 HIS A 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.199102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.177161 restraints weight = 5751.850| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.40 r_work: 0.3754 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6492 Z= 0.246 Angle : 0.603 8.035 8917 Z= 0.336 Chirality : 0.043 0.164 995 Planarity : 0.004 0.049 1020 Dihedral : 16.492 136.999 1111 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.55 % Favored : 93.30 % Rotamer: Outliers : 5.43 % Allowed : 17.93 % Favored : 76.64 % 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: -0.42 (0.31), residues: 687 helix: 0.57 (0.32), residues: 254 sheet: 0.77 (0.44), residues: 122 loop : -1.44 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 43 HIS 0.003 0.001 HIS A 590 PHE 0.016 0.002 PHE A 351 TYR 0.009 0.001 TYR A 690 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.542 Fit side-chains REVERT: A 82 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7245 (mp) REVERT: A 105 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6851 (mmt90) REVERT: A 126 GLN cc_start: 0.7211 (tt0) cc_final: 0.6858 (tm-30) REVERT: A 128 ILE cc_start: 0.6359 (OUTLIER) cc_final: 0.6099 (mt) REVERT: A 133 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7030 (tt) REVERT: A 464 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7142 (mp) REVERT: A 721 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7554 (mtt-85) outliers start: 33 outliers final: 15 residues processed: 84 average time/residue: 1.0566 time to fit residues: 94.0364 Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 724 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.0010 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 178 HIS A 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.200433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.174899 restraints weight = 5753.840| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.62 r_work: 0.3749 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6492 Z= 0.206 Angle : 0.582 8.918 8917 Z= 0.324 Chirality : 0.042 0.158 995 Planarity : 0.004 0.043 1020 Dihedral : 16.357 135.606 1111 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.40 % Favored : 93.45 % Rotamer: Outliers : 3.62 % Allowed : 19.74 % Favored : 76.64 % 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: -0.25 (0.32), residues: 687 helix: 0.67 (0.33), residues: 258 sheet: 0.89 (0.44), residues: 122 loop : -1.34 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 43 HIS 0.003 0.001 HIS A 590 PHE 0.010 0.001 PHE A 351 TYR 0.008 0.001 TYR A 617 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.656 Fit side-chains REVERT: A 82 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7173 (mp) REVERT: A 105 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6818 (mmt90) REVERT: A 124 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.5910 (pp) REVERT: A 128 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6077 (mt) REVERT: A 133 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7013 (tt) REVERT: A 464 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7167 (mp) REVERT: A 575 GLN cc_start: 0.7019 (pp30) cc_final: 0.6759 (pp30) outliers start: 22 outliers final: 11 residues processed: 77 average time/residue: 1.0018 time to fit residues: 82.2960 Evaluate side-chains 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.198283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.176507 restraints weight = 5792.789| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.38 r_work: 0.3730 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6492 Z= 0.296 Angle : 0.650 8.864 8917 Z= 0.359 Chirality : 0.044 0.173 995 Planarity : 0.004 0.049 1020 Dihedral : 16.604 139.178 1111 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.70 % Favored : 93.16 % Rotamer: Outliers : 3.95 % Allowed : 19.74 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.31), residues: 687 helix: 0.55 (0.33), residues: 254 sheet: 0.80 (0.45), residues: 122 loop : -1.47 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 43 HIS 0.003 0.001 HIS A 320 PHE 0.014 0.002 PHE A 101 TYR 0.011 0.002 TYR A 440 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.665 Fit side-chains REVERT: A 82 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7150 (mp) REVERT: A 105 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6880 (mmt90) REVERT: A 126 GLN cc_start: 0.7315 (tt0) cc_final: 0.6873 (tm-30) REVERT: A 128 ILE cc_start: 0.6385 (OUTLIER) cc_final: 0.6127 (mt) REVERT: A 133 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7004 (tt) REVERT: A 464 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7125 (mp) outliers start: 24 outliers final: 13 residues processed: 75 average time/residue: 1.0413 time to fit residues: 83.0555 Evaluate side-chains 76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 724 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.200779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.177871 restraints weight = 5838.173| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.47 r_work: 0.3766 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6492 Z= 0.217 Angle : 0.589 7.814 8917 Z= 0.329 Chirality : 0.042 0.159 995 Planarity : 0.004 0.040 1020 Dihedral : 16.429 136.349 1111 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.70 % Favored : 93.16 % Rotamer: Outliers : 3.12 % Allowed : 20.07 % Favored : 76.81 % 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: -0.33 (0.31), residues: 687 helix: 0.56 (0.33), residues: 257 sheet: 0.94 (0.45), residues: 122 loop : -1.38 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 43 HIS 0.003 0.001 HIS A 710 PHE 0.010 0.002 PHE A 351 TYR 0.012 0.001 TYR A 158 ARG 0.005 0.000 ARG A 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.622 Fit side-chains REVERT: A 82 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7206 (mp) REVERT: A 105 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6843 (mmt90) REVERT: A 124 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.5944 (pp) REVERT: A 126 GLN cc_start: 0.7292 (tt0) cc_final: 0.6907 (tm-30) REVERT: A 128 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.6065 (mt) REVERT: A 133 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7016 (tt) REVERT: A 464 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7157 (mp) outliers start: 19 outliers final: 11 residues processed: 73 average time/residue: 1.0360 time to fit residues: 80.5453 Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 724 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 10 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 376 GLN A 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.203850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178579 restraints weight = 5891.591| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.66 r_work: 0.3736 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6492 Z= 0.149 Angle : 0.535 7.409 8917 Z= 0.301 Chirality : 0.041 0.148 995 Planarity : 0.004 0.035 1020 Dihedral : 16.145 129.481 1111 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.11 % Favored : 93.74 % Rotamer: Outliers : 3.29 % Allowed : 20.23 % Favored : 76.48 % 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: -0.11 (0.32), residues: 687 helix: 0.91 (0.33), residues: 253 sheet: 0.92 (0.42), residues: 139 loop : -1.46 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 43 HIS 0.003 0.000 HIS A 590 PHE 0.013 0.001 PHE A 319 TYR 0.013 0.001 TYR A 158 ARG 0.004 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4025.92 seconds wall clock time: 71 minutes 54.15 seconds (4314.15 seconds total)