Starting phenix.real_space_refine on Wed Sep 17 19:55:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjx_38409/09_2025/8xjx_38409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjx_38409/09_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_38409/09_2025/8xjx_38409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjx_38409/09_2025/8xjx_38409.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjx_38409/09_2025/8xjx_38409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjx_38409/09_2025/8xjx_38409.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, '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: 1.52, per 1000 atoms: 0.24 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: 0.49 Conformation dependent library (CDL) restraints added in 320.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.74 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: 1.25 Time building geometry restraints manager: 0.64 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.780 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- 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= 0.160 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (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 ARG 0.004 0.000 ARG A 175 TYR 0.009 0.001 TYR A 53 PHE 0.017 0.001 PHE A 351 TRP 0.024 0.002 TRP A 43 HIS 0.003 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6492) covalent geometry : angle 0.60124 ( 8917) hydrogen bonds : bond 0.12717 ( 267) hydrogen bonds : angle 6.37829 ( 734) *********************** 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 : 0.195 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: 0.5786 time to fit residues: 67.8592 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 : 0.239 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0470 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- 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 675 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.202785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.186466 restraints weight = 5753.947| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.22 r_work: 0.3870 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6492 Z= 0.161 Angle : 0.585 5.832 8917 Z= 0.329 Chirality : 0.043 0.158 995 Planarity : 0.004 0.050 1020 Dihedral : 16.414 136.492 1117 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.68 % Favored : 94.03 % Rotamer: Outliers : 2.80 % Allowed : 11.68 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.31), residues: 687 helix: 0.85 (0.32), residues: 253 sheet: 0.95 (0.42), residues: 122 loop : -1.42 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.009 0.001 TYR A 690 PHE 0.015 0.002 PHE A 253 TRP 0.017 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6492) covalent geometry : angle 0.58499 ( 8917) hydrogen bonds : bond 0.04409 ( 267) hydrogen bonds : angle 4.96704 ( 734) *********************** 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 91 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.244 Fit side-chains REVERT: A 111 ARG cc_start: 0.7819 (ptm160) cc_final: 0.7593 (mtp-110) REVERT: A 122 GLN cc_start: 0.6130 (tt0) cc_final: 0.5869 (mt0) REVERT: A 400 HIS cc_start: 0.7360 (m90) cc_final: 0.7138 (m90) REVERT: A 414 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: A 464 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6769 (mp) REVERT: A 532 ASN cc_start: 0.7613 (m-40) cc_final: 0.7374 (m-40) REVERT: A 667 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7407 (ttt) outliers start: 17 outliers final: 3 residues processed: 82 average time/residue: 0.5359 time to fit residues: 46.2322 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 435 GLN A 510 GLN A 548 HIS A 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.203615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.178822 restraints weight = 5732.554| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.59 r_work: 0.3827 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6492 Z= 0.135 Angle : 0.554 7.934 8917 Z= 0.312 Chirality : 0.041 0.152 995 Planarity : 0.004 0.041 1020 Dihedral : 16.028 134.508 1114 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 3.45 % Allowed : 13.49 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.31), residues: 687 helix: 0.99 (0.33), residues: 256 sheet: 1.11 (0.43), residues: 122 loop : -1.37 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.009 0.001 TYR A 158 PHE 0.013 0.001 PHE A 351 TRP 0.014 0.001 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6492) covalent geometry : angle 0.55407 ( 8917) hydrogen bonds : bond 0.03989 ( 267) hydrogen bonds : angle 4.82483 ( 734) *********************** 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 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.212 Fit side-chains REVERT: A 67 MET cc_start: 0.6551 (tpp) cc_final: 0.6321 (tpt) REVERT: A 111 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7616 (mtp-110) REVERT: A 126 GLN cc_start: 0.7270 (tt0) cc_final: 0.6636 (tm-30) REVERT: A 155 GLU cc_start: 0.6725 (tt0) cc_final: 0.6475 (tp30) REVERT: A 464 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6952 (mp) REVERT: A 532 ASN cc_start: 0.7625 (m-40) cc_final: 0.7409 (m-40) outliers start: 21 outliers final: 8 residues processed: 79 average time/residue: 0.4846 time to fit residues: 40.6379 Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 575 GLN Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 51 optimal weight: 0.0020 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN A 510 GLN A 548 HIS A 675 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.205050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.179187 restraints weight = 5770.651| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.68 r_work: 0.3747 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6492 Z= 0.116 Angle : 0.526 6.034 8917 Z= 0.297 Chirality : 0.041 0.147 995 Planarity : 0.003 0.038 1020 Dihedral : 15.836 120.467 1114 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.47 % Rotamer: Outliers : 3.29 % Allowed : 13.65 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.32), residues: 687 helix: 1.16 (0.34), residues: 255 sheet: 1.25 (0.44), residues: 122 loop : -1.31 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.009 0.001 TYR A 158 PHE 0.019 0.001 PHE A 351 TRP 0.012 0.001 TRP A 43 HIS 0.003 0.000 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6492) covalent geometry : angle 0.52595 ( 8917) hydrogen bonds : bond 0.03492 ( 267) hydrogen bonds : angle 4.69358 ( 734) *********************** 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 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.234 Fit side-chains REVERT: A 126 GLN cc_start: 0.7080 (tt0) cc_final: 0.6626 (tm-30) REVERT: A 155 GLU cc_start: 0.6511 (tt0) cc_final: 0.6303 (tp30) REVERT: A 464 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7125 (mp) REVERT: A 532 ASN cc_start: 0.7581 (m-40) cc_final: 0.7378 (m-40) outliers start: 20 outliers final: 8 residues processed: 78 average time/residue: 0.4582 time to fit residues: 38.0718 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 148 PHE 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 575 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 370 GLN A 510 GLN A 541 ASN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.200096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.183930 restraints weight = 5858.629| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 1.28 r_work: 0.3739 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6492 Z= 0.183 Angle : 0.601 6.978 8917 Z= 0.335 Chirality : 0.043 0.164 995 Planarity : 0.004 0.050 1020 Dihedral : 16.265 127.397 1114 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.26 % Favored : 93.60 % Rotamer: Outliers : 4.44 % Allowed : 13.65 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.31), residues: 687 helix: 0.93 (0.33), residues: 255 sheet: 1.49 (0.46), residues: 102 loop : -1.39 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.010 0.001 TYR A 690 PHE 0.018 0.002 PHE A 351 TRP 0.020 0.002 TRP A 43 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 6492) covalent geometry : angle 0.60098 ( 8917) hydrogen bonds : bond 0.04614 ( 267) hydrogen bonds : angle 4.94709 ( 734) *********************** 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 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.215 Fit side-chains REVERT: A 126 GLN cc_start: 0.7316 (tt0) cc_final: 0.6515 (tm-30) REVERT: A 133 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7046 (tt) REVERT: A 155 GLU cc_start: 0.6784 (tt0) cc_final: 0.6351 (tp30) REVERT: A 414 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: A 464 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6647 (mp) REVERT: A 532 ASN cc_start: 0.7799 (m-40) cc_final: 0.7517 (m-40) outliers start: 27 outliers final: 12 residues processed: 86 average time/residue: 0.4999 time to fit residues: 45.5531 Evaluate side-chains 73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 148 PHE 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 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 Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 724 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.199033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.173558 restraints weight = 5828.326| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.63 r_work: 0.3758 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6492 Z= 0.198 Angle : 0.626 7.978 8917 Z= 0.348 Chirality : 0.044 0.169 995 Planarity : 0.004 0.053 1020 Dihedral : 16.417 131.494 1111 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.40 % Favored : 93.45 % Rotamer: Outliers : 4.28 % Allowed : 14.80 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.31), residues: 687 helix: 0.79 (0.33), residues: 253 sheet: 1.10 (0.44), residues: 119 loop : -1.46 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.010 0.002 TYR A 690 PHE 0.014 0.002 PHE A 101 TRP 0.024 0.002 TRP A 43 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 6492) covalent geometry : angle 0.62581 ( 8917) hydrogen bonds : bond 0.04835 ( 267) hydrogen bonds : angle 5.08262 ( 734) *********************** 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 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.164 Fit side-chains REVERT: A 82 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7118 (mp) REVERT: A 126 GLN cc_start: 0.7233 (tt0) cc_final: 0.6865 (tm-30) REVERT: A 133 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7025 (tt) REVERT: A 464 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7185 (mp) outliers start: 26 outliers final: 12 residues processed: 85 average time/residue: 0.5340 time to fit residues: 47.7425 Evaluate side-chains 76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 133 ILE Chi-restraints excluded: chain A residue 148 PHE 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 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 724 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 0.0040 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.0194 ------------------------------------------------------------------------------- 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 A 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.201450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.176163 restraints weight = 5769.172| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.63 r_work: 0.3700 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2705 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= 0.142 Angle : 0.565 6.605 8917 Z= 0.317 Chirality : 0.042 0.153 995 Planarity : 0.004 0.045 1020 Dihedral : 16.245 129.309 1111 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.89 % Rotamer: Outliers : 3.29 % Allowed : 17.60 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.32), residues: 687 helix: 0.84 (0.33), residues: 255 sheet: 0.99 (0.43), residues: 133 loop : -1.42 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.009 0.001 TYR A 20 PHE 0.014 0.001 PHE A 351 TRP 0.022 0.002 TRP A 43 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6492) covalent geometry : angle 0.56473 ( 8917) hydrogen bonds : bond 0.04061 ( 267) hydrogen bonds : angle 4.94259 ( 734) *********************** 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 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.188 Fit side-chains REVERT: A 126 GLN cc_start: 0.7204 (tt0) cc_final: 0.6834 (tm-30) REVERT: A 133 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7026 (tt) REVERT: A 464 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7219 (mp) outliers start: 20 outliers final: 13 residues processed: 74 average time/residue: 0.5320 time to fit residues: 41.6768 Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 148 PHE 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 692 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 66 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 79 HIS A 510 GLN A 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.198623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.174500 restraints weight = 5766.043| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 1.53 r_work: 0.3678 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6492 Z= 0.209 Angle : 0.640 7.444 8917 Z= 0.356 Chirality : 0.045 0.174 995 Planarity : 0.004 0.051 1020 Dihedral : 16.495 132.745 1111 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.70 % Favored : 93.16 % Rotamer: Outliers : 4.44 % Allowed : 17.11 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.31), residues: 687 helix: 0.62 (0.33), residues: 253 sheet: 0.89 (0.45), residues: 121 loop : -1.43 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.012 0.002 TYR A 20 PHE 0.015 0.002 PHE A 351 TRP 0.031 0.002 TRP A 43 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 6492) covalent geometry : angle 0.63980 ( 8917) hydrogen bonds : bond 0.04967 ( 267) hydrogen bonds : angle 5.09889 ( 734) *********************** 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 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.233 Fit side-chains REVERT: A 82 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7137 (mp) REVERT: A 124 ILE cc_start: 0.6365 (OUTLIER) cc_final: 0.5947 (pp) REVERT: A 126 GLN cc_start: 0.7236 (tt0) cc_final: 0.6771 (tm-30) REVERT: A 128 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6045 (mt) REVERT: A 133 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7049 (tt) REVERT: A 464 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7087 (mp) outliers start: 27 outliers final: 14 residues processed: 82 average time/residue: 0.4305 time to fit residues: 37.6828 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 : 0.304 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 148 PHE 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 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 575 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 724 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 0.0050 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 A 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.202515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.177409 restraints weight = 5863.859| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.66 r_work: 0.3719 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6492 Z= 0.127 Angle : 0.563 8.773 8917 Z= 0.314 Chirality : 0.042 0.149 995 Planarity : 0.004 0.039 1020 Dihedral : 16.200 127.805 1111 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.26 % Favored : 93.60 % Rotamer: Outliers : 4.11 % Allowed : 18.26 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.32), residues: 687 helix: 0.82 (0.33), residues: 255 sheet: 1.03 (0.45), residues: 122 loop : -1.26 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.008 0.001 TYR A 20 PHE 0.013 0.001 PHE A 319 TRP 0.026 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6492) covalent geometry : angle 0.56293 ( 8917) hydrogen bonds : bond 0.03772 ( 267) hydrogen bonds : angle 4.89671 ( 734) *********************** 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 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.262 Fit side-chains REVERT: A 82 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7007 (mp) REVERT: A 128 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.6031 (mt) REVERT: A 133 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7019 (tt) REVERT: A 464 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7138 (mp) REVERT: A 497 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7896 (mmm) outliers start: 25 outliers final: 13 residues processed: 78 average time/residue: 0.4380 time to fit residues: 36.5112 Evaluate side-chains 75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 148 PHE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 170 ILE 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 464 LEU Chi-restraints excluded: chain A residue 497 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 79 HIS A 510 GLN A 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.197854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.174772 restraints weight = 5801.386| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.46 r_work: 0.3728 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6492 Z= 0.228 Angle : 0.672 8.304 8917 Z= 0.373 Chirality : 0.046 0.181 995 Planarity : 0.005 0.050 1020 Dihedral : 16.587 132.750 1111 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.70 % Favored : 93.16 % Rotamer: Outliers : 3.78 % Allowed : 18.42 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.31), residues: 687 helix: 0.51 (0.33), residues: 253 sheet: 0.90 (0.45), residues: 121 loop : -1.48 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 175 TYR 0.012 0.002 TYR A 20 PHE 0.016 0.002 PHE A 101 TRP 0.043 0.003 TRP A 43 HIS 0.005 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 6492) covalent geometry : angle 0.67202 ( 8917) hydrogen bonds : bond 0.05233 ( 267) hydrogen bonds : angle 5.17972 ( 734) ********************** 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 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.234 Fit side-chains REVERT: A 82 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7085 (mp) REVERT: A 124 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.5917 (pp) REVERT: A 126 GLN cc_start: 0.7415 (tt0) cc_final: 0.6915 (tm-30) REVERT: A 128 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.6073 (mt) REVERT: A 133 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7016 (tt) REVERT: A 464 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7069 (mp) outliers start: 23 outliers final: 14 residues processed: 74 average time/residue: 0.4298 time to fit residues: 33.9447 Evaluate side-chains 80 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 148 PHE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 170 ILE 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 575 GLN Chi-restraints excluded: chain A residue 685 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 79 HIS A 376 GLN A 510 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.202065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178319 restraints weight = 5798.814| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.53 r_work: 0.3733 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6492 Z= 0.133 Angle : 0.569 7.839 8917 Z= 0.320 Chirality : 0.042 0.150 995 Planarity : 0.004 0.039 1020 Dihedral : 16.241 127.037 1111 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.26 % Favored : 93.60 % Rotamer: Outliers : 3.45 % Allowed : 18.91 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.32), residues: 687 helix: 0.81 (0.33), residues: 255 sheet: 1.06 (0.45), residues: 122 loop : -1.34 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.012 0.001 TYR A 493 PHE 0.014 0.001 PHE A 319 TRP 0.039 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6492) covalent geometry : angle 0.56942 ( 8917) hydrogen bonds : bond 0.03895 ( 267) hydrogen bonds : angle 4.92944 ( 734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2031.49 seconds wall clock time: 35 minutes 20.40 seconds (2120.40 seconds total)