Starting phenix.real_space_refine on Wed Jul 1 22:20:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhq_36284/07_2026/8jhq_36284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhq_36284/07_2026/8jhq_36284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jhq_36284/07_2026/8jhq_36284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhq_36284/07_2026/8jhq_36284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jhq_36284/07_2026/8jhq_36284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhq_36284/07_2026/8jhq_36284.map" } resolution = 3.6 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= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 19 5.16 5 C 2235 2.51 5 N 571 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3420 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3395 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 14, 'TRANS': 431} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.85, per 1000 atoms: 0.25 Number of scatterers: 3420 At special positions: 0 Unit cell: (88.4, 62.9, 66.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 1 15.00 O 594 8.00 N 571 7.00 C 2235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 554 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 129.3 milliseconds 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.892A pdb=" N ALA A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.828A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.725A pdb=" N ARG A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 192 through 212 removed outlier: 3.590A pdb=" N LEU A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.579A pdb=" N ILE A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 453 removed outlier: 4.377A pdb=" N ILE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 454 through 460 removed outlier: 3.543A pdb=" N TRP A 457 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 removed outlier: 4.315A pdb=" N LEU A 465 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 471 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 removed outlier: 3.576A pdb=" N ALA A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 543 Proline residue: A 533 - end of helix Processing helix chain 'A' and resid 556 through 586 removed outlier: 3.547A pdb=" N LEU A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 571 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 614 removed outlier: 3.894A pdb=" N PHE A 611 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 612 " --> pdb=" O CYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 634 removed outlier: 4.009A pdb=" N ALA A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 647 removed outlier: 3.650A pdb=" N ALA A 640 " --> pdb=" O TRP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 666 removed outlier: 4.403A pdb=" N ALA A 653 " --> pdb=" O PRO A 649 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR A 654 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 685 removed outlier: 3.917A pdb=" N SER A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 702 Processing helix chain 'A' and resid 702 through 737 removed outlier: 4.374A pdb=" N PHE A 706 " --> pdb=" O MET A 702 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.53 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1059 1.34 - 1.46: 883 1.46 - 1.58: 1526 1.58 - 1.70: 1 1.70 - 1.82: 28 Bond restraints: 3497 Sorted by residual: bond pdb=" C3 S1P A 801 " pdb=" O3 S1P A 801 " ideal model delta sigma weight residual 1.445 1.400 0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" N MET A 426 " pdb=" CA MET A 426 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.19e-02 7.06e+03 3.69e+00 bond pdb=" N GLN A 659 " pdb=" CA GLN A 659 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.20e-02 6.94e+03 2.74e+00 bond pdb=" C3 S1P A 801 " pdb=" C4 S1P A 801 " ideal model delta sigma weight residual 1.496 1.528 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" O1 S1P A 801 " pdb=" P22 S1P A 801 " ideal model delta sigma weight residual 1.677 1.647 0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 3492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 4631 1.76 - 3.52: 69 3.52 - 5.28: 35 5.28 - 7.04: 8 7.04 - 8.80: 3 Bond angle restraints: 4746 Sorted by residual: angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.68 114.31 6.37 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N GLN A 659 " pdb=" CA GLN A 659 " pdb=" C GLN A 659 " ideal model delta sigma weight residual 111.11 107.31 3.80 1.20e+00 6.94e-01 1.00e+01 angle pdb=" N ILE A 565 " pdb=" CA ILE A 565 " pdb=" CB ILE A 565 " ideal model delta sigma weight residual 110.54 114.76 -4.22 1.36e+00 5.41e-01 9.61e+00 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 119.40 -5.80 1.90e+00 2.77e-01 9.33e+00 angle pdb=" CB MET A 467 " pdb=" CG MET A 467 " pdb=" SD MET A 467 " ideal model delta sigma weight residual 112.70 121.50 -8.80 3.00e+00 1.11e-01 8.60e+00 ... (remaining 4741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.52: 1939 33.52 - 67.04: 82 67.04 - 100.55: 4 100.55 - 134.07: 4 134.07 - 167.59: 4 Dihedral angle restraints: 2033 sinusoidal: 768 harmonic: 1265 Sorted by residual: dihedral pdb=" C3 S1P A 801 " pdb=" C1 S1P A 801 " pdb=" C2 S1P A 801 " pdb=" O1 S1P A 801 " ideal model delta sinusoidal sigma weight residual 52.36 -115.23 167.59 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C12 S1P A 801 " pdb=" C13 S1P A 801 " pdb=" C14 S1P A 801 " pdb=" C15 S1P A 801 " ideal model delta sinusoidal sigma weight residual 300.92 134.42 166.50 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C2 S1P A 801 " pdb=" C1 S1P A 801 " pdb=" O1 S1P A 801 " pdb=" P22 S1P A 801 " ideal model delta sinusoidal sigma weight residual 262.13 95.94 166.19 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 428 0.046 - 0.092: 103 0.092 - 0.138: 19 0.138 - 0.183: 4 0.183 - 0.229: 1 Chirality restraints: 555 Sorted by residual: chirality pdb=" CB THR A 444 " pdb=" CA THR A 444 " pdb=" OG1 THR A 444 " pdb=" CG2 THR A 444 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C2 S1P A 801 " pdb=" C1 S1P A 801 " pdb=" C3 S1P A 801 " pdb=" N2 S1P A 801 " both_signs ideal model delta sigma weight residual False -2.43 -2.60 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CB ILE A 565 " pdb=" CA ILE A 565 " pdb=" CG1 ILE A 565 " pdb=" CG2 ILE A 565 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 552 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.029 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP A 178 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 552 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 553 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 658 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C LEU A 658 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU A 658 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN A 659 " 0.008 2.00e-02 2.50e+03 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 264 2.74 - 3.28: 3575 3.28 - 3.82: 5734 3.82 - 4.36: 5997 4.36 - 4.90: 10767 Nonbonded interactions: 26337 Sorted by model distance: nonbonded pdb=" OE1 GLN A 543 " pdb=" OG1 THR A 545 " model vdw 2.196 3.040 nonbonded pdb=" ND2 ASN A 115 " pdb=" OE1 GLU A 207 " model vdw 2.205 3.120 nonbonded pdb=" O ILE A 443 " pdb=" OG SER A 447 " model vdw 2.262 3.040 nonbonded pdb=" OG SER A 145 " pdb=" O ALA A 669 " model vdw 2.331 3.040 nonbonded pdb=" N ASP A 668 " pdb=" OD1 ASP A 668 " model vdw 2.345 3.120 ... (remaining 26332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.120 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 0.052 3498 Z= 0.163 Angle : 0.686 8.798 4748 Z= 0.342 Chirality : 0.042 0.229 555 Planarity : 0.004 0.049 584 Dihedral : 20.424 167.586 1222 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 30.06 % Favored : 69.94 % 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 are not related in a simple way. whole: 1.50 (0.42), residues: 442 helix: 1.63 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.52 (0.75), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 726 TYR 0.018 0.001 TYR A 645 PHE 0.023 0.001 PHE A 222 TRP 0.064 0.002 TRP A 178 HIS 0.003 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 3497) covalent geometry : angle 0.68564 / 0.34 ( 4746) SS BOND : bond 0.00142 / 0.07 ( 1) SS BOND : angle 1.23659 / 0.82 ( 2) hydrogen bonds : bond 0.14688 / 10.89 ( 270) hydrogen bonds : angle 5.99304 / 4.28 ( 801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.129 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0477 time to fit residues: 3.9681 Evaluate side-chains 59 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115598 restraints weight = 4761.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119515 restraints weight = 2714.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122075 restraints weight = 1934.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123465 restraints weight = 1582.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124097 restraints weight = 1410.569| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3498 Z= 0.149 Angle : 0.582 7.730 4748 Z= 0.304 Chirality : 0.040 0.162 555 Planarity : 0.004 0.052 584 Dihedral : 14.789 161.284 504 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.93 % Allowed : 25.28 % Favored : 70.79 % 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 are not related in a simple way. whole: 2.04 (0.41), residues: 442 helix: 2.07 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.00 (0.74), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 726 TYR 0.016 0.001 TYR A 645 PHE 0.015 0.001 PHE A 222 TRP 0.040 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 3497) covalent geometry : angle 0.57929 / 0.30 ( 4746) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 2.56529 / 1.71 ( 2) hydrogen bonds : bond 0.05325 / 3.57 ( 270) hydrogen bonds : angle 4.41328 / 3.20 ( 801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7919 (m-80) cc_final: 0.7519 (m-80) REVERT: A 207 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 543 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7741 (tm-30) outliers start: 14 outliers final: 8 residues processed: 73 average time/residue: 0.0417 time to fit residues: 4.1508 Evaluate side-chains 68 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115318 restraints weight = 4724.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119247 restraints weight = 2670.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121463 restraints weight = 1902.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123332 restraints weight = 1571.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124016 restraints weight = 1383.565| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.142 Angle : 0.560 7.146 4748 Z= 0.294 Chirality : 0.039 0.173 555 Planarity : 0.004 0.049 584 Dihedral : 13.558 154.599 504 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.21 % Allowed : 26.40 % Favored : 69.38 % 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 are not related in a simple way. whole: 2.17 (0.41), residues: 442 helix: 2.16 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.99 (0.76), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 726 TYR 0.020 0.002 TYR A 160 PHE 0.013 0.001 PHE A 523 TRP 0.040 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 3497) covalent geometry : angle 0.55859 / 0.29 ( 4746) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 2.09688 / 1.40 ( 2) hydrogen bonds : bond 0.05031 / 3.34 ( 270) hydrogen bonds : angle 4.19059 / 3.06 ( 801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8818 (mp) REVERT: A 192 TYR cc_start: 0.7932 (m-80) cc_final: 0.7609 (m-80) REVERT: A 207 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7863 (mm-30) outliers start: 15 outliers final: 9 residues processed: 76 average time/residue: 0.0514 time to fit residues: 5.0682 Evaluate side-chains 70 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104637 restraints weight = 5009.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108453 restraints weight = 2920.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110835 restraints weight = 2116.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112500 restraints weight = 1755.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112867 restraints weight = 1563.812| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3498 Z= 0.146 Angle : 0.578 7.831 4748 Z= 0.303 Chirality : 0.040 0.185 555 Planarity : 0.004 0.050 584 Dihedral : 12.958 148.879 504 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.06 % Allowed : 26.40 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.41), residues: 442 helix: 2.15 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.97 (0.77), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 726 TYR 0.017 0.002 TYR A 645 PHE 0.013 0.001 PHE A 523 TRP 0.040 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 3497) covalent geometry : angle 0.57719 / 0.30 ( 4746) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 1.92795 / 1.29 ( 2) hydrogen bonds : bond 0.05044 / 3.36 ( 270) hydrogen bonds : angle 4.12079 / 3.02 ( 801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (mp) REVERT: A 192 TYR cc_start: 0.8016 (m-80) cc_final: 0.7694 (m-80) REVERT: A 207 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8314 (mm-30) outliers start: 18 outliers final: 12 residues processed: 75 average time/residue: 0.0400 time to fit residues: 3.9980 Evaluate side-chains 73 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102278 restraints weight = 5061.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106321 restraints weight = 2790.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108898 restraints weight = 1958.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110410 restraints weight = 1591.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110941 restraints weight = 1413.159| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3498 Z= 0.152 Angle : 0.580 5.768 4748 Z= 0.307 Chirality : 0.040 0.192 555 Planarity : 0.004 0.050 584 Dihedral : 12.735 147.465 504 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.34 % Allowed : 26.69 % Favored : 67.98 % 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 are not related in a simple way. whole: 2.19 (0.41), residues: 442 helix: 2.17 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.96 (0.77), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 726 TYR 0.020 0.002 TYR A 160 PHE 0.013 0.001 PHE A 523 TRP 0.040 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 3497) covalent geometry : angle 0.57716 / 0.31 ( 4746) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 2.77669 / 1.85 ( 2) hydrogen bonds : bond 0.05145 / 3.41 ( 270) hydrogen bonds : angle 4.13976 / 3.03 ( 801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: A 192 TYR cc_start: 0.8084 (m-80) cc_final: 0.7773 (m-80) REVERT: A 207 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8300 (mm-30) outliers start: 19 outliers final: 13 residues processed: 71 average time/residue: 0.0369 time to fit residues: 3.4663 Evaluate side-chains 72 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107579 restraints weight = 4961.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111483 restraints weight = 2827.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114046 restraints weight = 2026.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115713 restraints weight = 1658.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116366 restraints weight = 1470.844| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3498 Z= 0.132 Angle : 0.563 5.897 4748 Z= 0.297 Chirality : 0.040 0.200 555 Planarity : 0.004 0.050 584 Dihedral : 12.459 145.239 504 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.49 % Allowed : 28.37 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.41), residues: 442 helix: 2.19 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.90 (0.76), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 726 TYR 0.016 0.001 TYR A 645 PHE 0.012 0.001 PHE A 523 TRP 0.038 0.002 TRP A 178 HIS 0.002 0.000 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 3497) covalent geometry : angle 0.56014 / 0.30 ( 4746) SS BOND : bond 0.00255 / 0.13 ( 1) SS BOND : angle 2.78297 / 1.86 ( 2) hydrogen bonds : bond 0.04698 / 3.10 ( 270) hydrogen bonds : angle 4.04670 / 2.96 ( 801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7986 (m-80) cc_final: 0.7722 (m-80) REVERT: A 207 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8252 (mm-30) REVERT: A 543 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7448 (tm-30) outliers start: 16 outliers final: 11 residues processed: 74 average time/residue: 0.0338 time to fit residues: 3.2697 Evaluate side-chains 69 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 39 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105429 restraints weight = 5135.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109374 restraints weight = 2919.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111916 restraints weight = 2090.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113586 restraints weight = 1713.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114347 restraints weight = 1524.055| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.003 0.032 3498 Z= 0.137 Angle : 0.577 7.679 4748 Z= 0.302 Chirality : 0.040 0.205 555 Planarity : 0.004 0.050 584 Dihedral : 12.266 144.739 504 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.21 % Allowed : 29.21 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.41), residues: 442 helix: 2.16 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -1.81 (0.77), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 726 TYR 0.022 0.001 TYR A 160 PHE 0.012 0.001 PHE A 523 TRP 0.039 0.002 TRP A 178 HIS 0.002 0.000 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 3497) covalent geometry : angle 0.57452 / 0.30 ( 4746) SS BOND : bond 0.00215 / 0.11 ( 1) SS BOND : angle 2.55557 / 1.70 ( 2) hydrogen bonds : bond 0.04833 / 3.20 ( 270) hydrogen bonds : angle 4.07598 / 2.99 ( 801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.8005 (m-80) cc_final: 0.7777 (m-80) REVERT: A 207 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8299 (mm-30) outliers start: 15 outliers final: 13 residues processed: 73 average time/residue: 0.0430 time to fit residues: 4.2045 Evaluate side-chains 73 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.0370 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0270 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108226 restraints weight = 5139.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112218 restraints weight = 2918.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114866 restraints weight = 2085.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116484 restraints weight = 1705.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117141 restraints weight = 1511.058| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3498 Z= 0.130 Angle : 0.603 11.365 4748 Z= 0.312 Chirality : 0.040 0.208 555 Planarity : 0.004 0.051 584 Dihedral : 11.801 143.380 504 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.65 % Allowed : 30.06 % Favored : 66.29 % 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 are not related in a simple way. whole: 2.37 (0.42), residues: 442 helix: 2.21 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.51 (0.82), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 726 TYR 0.017 0.001 TYR A 645 PHE 0.012 0.001 PHE A 523 TRP 0.037 0.002 TRP A 178 HIS 0.002 0.000 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 3497) covalent geometry : angle 0.60099 / 0.31 ( 4746) SS BOND : bond 0.00212 / 0.11 ( 1) SS BOND : angle 2.58023 / 1.72 ( 2) hydrogen bonds : bond 0.04488 / 2.98 ( 270) hydrogen bonds : angle 4.01147 / 2.96 ( 801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8233 (mm-30) REVERT: A 633 PHE cc_start: 0.8608 (m-10) cc_final: 0.8156 (m-10) outliers start: 13 outliers final: 12 residues processed: 69 average time/residue: 0.0303 time to fit residues: 2.8127 Evaluate side-chains 73 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 50.0000 chunk 27 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106195 restraints weight = 5059.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110156 restraints weight = 2899.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112730 restraints weight = 2084.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114072 restraints weight = 1709.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115223 restraints weight = 1530.534| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3498 Z= 0.146 Angle : 0.623 11.515 4748 Z= 0.321 Chirality : 0.041 0.217 555 Planarity : 0.004 0.051 584 Dihedral : 11.645 143.997 504 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.21 % Allowed : 30.06 % Favored : 65.73 % 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 are not related in a simple way. whole: 2.29 (0.42), residues: 442 helix: 2.15 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.52 (0.82), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 726 TYR 0.024 0.002 TYR A 160 PHE 0.013 0.001 PHE A 523 TRP 0.039 0.002 TRP A 178 HIS 0.001 0.000 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 3497) covalent geometry : angle 0.62164 / 0.32 ( 4746) SS BOND : bond 0.00198 / 0.10 ( 1) SS BOND : angle 2.41896 / 1.61 ( 2) hydrogen bonds : bond 0.04899 / 3.25 ( 270) hydrogen bonds : angle 4.10197 / 3.03 ( 801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8277 (mm-30) outliers start: 15 outliers final: 14 residues processed: 70 average time/residue: 0.0481 time to fit residues: 4.5132 Evaluate side-chains 74 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104505 restraints weight = 5058.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108621 restraints weight = 2742.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111356 restraints weight = 1913.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113019 restraints weight = 1546.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113712 restraints weight = 1365.117| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 3498 Z= 0.157 Angle : 0.642 11.754 4748 Z= 0.333 Chirality : 0.042 0.226 555 Planarity : 0.004 0.051 584 Dihedral : 11.285 144.429 504 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.93 % Allowed : 30.34 % Favored : 65.73 % 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 are not related in a simple way. whole: 2.21 (0.42), residues: 442 helix: 2.11 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.58 (0.82), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 726 TYR 0.019 0.002 TYR A 535 PHE 0.014 0.001 PHE A 626 TRP 0.040 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 3497) covalent geometry : angle 0.63999 / 0.33 ( 4746) SS BOND : bond 0.00209 / 0.11 ( 1) SS BOND : angle 2.55783 / 1.71 ( 2) hydrogen bonds : bond 0.05158 / 3.43 ( 270) hydrogen bonds : angle 4.18757 / 3.10 ( 801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7472 (ttm) cc_final: 0.7259 (ttt) REVERT: A 207 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8315 (mm-30) outliers start: 14 outliers final: 14 residues processed: 70 average time/residue: 0.0480 time to fit residues: 4.4952 Evaluate side-chains 75 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104519 restraints weight = 5100.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108395 restraints weight = 2875.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110688 restraints weight = 2052.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112372 restraints weight = 1689.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113065 restraints weight = 1503.814| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 3498 Z= 0.153 Angle : 0.637 11.853 4748 Z= 0.330 Chirality : 0.042 0.239 555 Planarity : 0.004 0.050 584 Dihedral : 10.875 144.548 504 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.49 % Allowed : 30.06 % Favored : 65.45 % 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 are not related in a simple way. whole: 2.23 (0.42), residues: 442 helix: 2.14 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.63 (0.82), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 726 TYR 0.008 0.001 TYR A 116 PHE 0.014 0.001 PHE A 626 TRP 0.039 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3497) covalent geometry : angle 0.63568 / 0.33 ( 4746) SS BOND : bond 0.00185 / 0.10 ( 1) SS BOND : angle 2.33220 / 1.55 ( 2) hydrogen bonds : bond 0.05029 / 3.34 ( 270) hydrogen bonds : angle 4.16404 / 3.08 ( 801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 709.72 seconds wall clock time: 12 minutes 54.42 seconds (774.42 seconds total)