Starting phenix.real_space_refine on Wed Jun 3 13:12:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vc9_64949/06_2026/9vc9_64949.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vc9_64949/06_2026/9vc9_64949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vc9_64949/06_2026/9vc9_64949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vc9_64949/06_2026/9vc9_64949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vc9_64949/06_2026/9vc9_64949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vc9_64949/06_2026/9vc9_64949.map" } resolution = 2.77 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= 0.003 sd= 0.146 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 Zn 1 6.06 5 S 16 5.16 5 C 3689 2.51 5 N 932 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5608 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5538 Classifications: {'peptide': 704} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 673} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' ZN': 1, 'AV0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.61, per 1000 atoms: 0.29 Number of scatterers: 5608 At special positions: 0 Unit cell: (78.5757, 91.8561, 107.35, 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) Zn 1 29.99 S 16 16.00 O 970 8.00 N 932 7.00 C 3689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 636 " distance=2.09 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: 0.42 Conformation dependent library (CDL) restraints added in 288.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" NE2 HIS A 580 " pdb="ZN ZN A 802 " - pdb=" NE2 HIS A 681 " 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1308 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 56.0% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.537A pdb=" N CYS A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 171 through 185 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 224 through 247 Processing helix chain 'A' and resid 250 through 274 Processing helix chain 'A' and resid 276 through 295 Processing helix chain 'A' and resid 300 through 316 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.603A pdb=" N TRP A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 383 Processing helix chain 'A' and resid 388 through 405 Proline residue: A 400 - end of helix Processing helix chain 'A' and resid 405 through 423 Processing helix chain 'A' and resid 428 through 451 removed outlier: 3.677A pdb=" N LEU A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 555 through 563 Processing helix chain 'A' and resid 577 through 582 Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 654 through 667 removed outlier: 3.956A pdb=" N LYS A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.729A pdb=" N ARG A 724 " --> pdb=" O ARG A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 735 Processing helix chain 'A' and resid 758 through 762 removed outlier: 3.807A pdb=" N ARG A 762 " --> pdb=" O TRP A 759 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 85 removed outlier: 6.892A pdb=" N ILE A 80 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE A 95 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU A 82 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP A 93 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS A 108 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLY A 158 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG A 110 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL A 160 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR A 112 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS A 162 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N GLN A 114 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 12.293A pdb=" N GLN A 164 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 128 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 163 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 126 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU A 165 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL A 124 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN A 123 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 595 through 598 removed outlier: 9.253A pdb=" N ASN A 595 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP A 569 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE A 597 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 571 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA A 536 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL A 572 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 538 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.543A pdb=" N PHE A 549 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 611 through 615 Processing sheet with id=AA5, first strand: chain 'A' and resid 763 through 765 removed outlier: 5.450A pdb=" N ARG A 765 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ASN A 771 " --> pdb=" O ARG A 765 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 918 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: 0.91 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1250 1.33 - 1.46: 1933 1.46 - 1.59: 2550 1.59 - 1.72: 0 1.72 - 1.86: 25 Bond restraints: 5758 Sorted by residual: bond pdb=" CA SER A 403 " pdb=" CB SER A 403 " ideal model delta sigma weight residual 1.528 1.472 0.056 1.59e-02 3.96e+03 1.24e+01 bond pdb=" CE1 HIS A 227 " pdb=" NE2 HIS A 227 " ideal model delta sigma weight residual 1.321 1.353 -0.032 1.00e-02 1.00e+04 1.04e+01 bond pdb=" CA SER A 45 " pdb=" CB SER A 45 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.59e-02 3.96e+03 1.04e+01 bond pdb=" C ILE A 640 " pdb=" O ILE A 640 " ideal model delta sigma weight residual 1.238 1.203 0.035 1.09e-02 8.42e+03 1.02e+01 bond pdb=" CA SER A 229 " pdb=" CB SER A 229 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.56e-02 4.11e+03 8.76e+00 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 5928 1.44 - 2.89: 1607 2.89 - 4.33: 253 4.33 - 5.78: 44 5.78 - 7.22: 7 Bond angle restraints: 7839 Sorted by residual: angle pdb=" C LYS A 201 " pdb=" N GLN A 202 " pdb=" CA GLN A 202 " ideal model delta sigma weight residual 120.44 126.07 -5.63 1.30e+00 5.92e-01 1.87e+01 angle pdb=" C LEU A 203 " pdb=" N ILE A 204 " pdb=" CA ILE A 204 " ideal model delta sigma weight residual 122.59 119.48 3.11 7.20e-01 1.93e+00 1.87e+01 angle pdb=" N SER A 45 " pdb=" CA SER A 45 " pdb=" C SER A 45 " ideal model delta sigma weight residual 111.36 106.67 4.69 1.09e+00 8.42e-01 1.85e+01 angle pdb=" N GLN A 146 " pdb=" CA GLN A 146 " pdb=" CB GLN A 146 " ideal model delta sigma weight residual 110.16 104.04 6.12 1.48e+00 4.57e-01 1.71e+01 angle pdb=" N PRO A 757 " pdb=" CA PRO A 757 " pdb=" CB PRO A 757 " ideal model delta sigma weight residual 102.36 99.29 3.07 7.80e-01 1.64e+00 1.55e+01 ... (remaining 7834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.81: 3298 27.81 - 55.62: 112 55.62 - 83.43: 11 83.43 - 111.24: 4 111.24 - 139.06: 2 Dihedral angle restraints: 3427 sinusoidal: 1400 harmonic: 2027 Sorted by residual: dihedral pdb=" CB CYS A 608 " pdb=" SG CYS A 608 " pdb=" SG CYS A 636 " pdb=" CB CYS A 636 " ideal model delta sinusoidal sigma weight residual 93.00 171.19 -78.19 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CA ILE A 677 " pdb=" C ILE A 677 " pdb=" N ALA A 678 " pdb=" CA ALA A 678 " ideal model delta harmonic sigma weight residual -180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CBQ AV0 A 801 " pdb=" CBT AV0 A 801 " pdb=" CCM AV0 A 801 " pdb=" OBV AV0 A 801 " ideal model delta sinusoidal sigma weight residual 306.95 167.89 139.06 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 3424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 394 0.043 - 0.087: 289 0.087 - 0.130: 155 0.130 - 0.174: 57 0.174 - 0.217: 12 Chirality restraints: 907 Sorted by residual: chirality pdb=" CB VAL A 83 " pdb=" CA VAL A 83 " pdb=" CG1 VAL A 83 " pdb=" CG2 VAL A 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA SER A 62 " pdb=" N SER A 62 " pdb=" C SER A 62 " pdb=" CB SER A 62 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA THR A 730 " pdb=" N THR A 730 " pdb=" C THR A 730 " pdb=" CB THR A 730 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 904 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 57 " -0.049 2.00e-02 2.50e+03 3.03e-02 1.60e+01 pdb=" CG PHE A 57 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 57 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 57 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A 57 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 57 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 57 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 53 " 0.014 2.00e-02 2.50e+03 2.41e-02 1.46e+01 pdb=" CG TRP A 53 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 53 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP A 53 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP A 53 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP A 53 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 53 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 53 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 53 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 53 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 596 " -0.044 2.00e-02 2.50e+03 2.38e-02 1.42e+01 pdb=" CG TRP A 596 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP A 596 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 596 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 596 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 596 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 596 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 596 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 596 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 596 " -0.010 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 3 2.42 - 3.04: 3437 3.04 - 3.66: 8279 3.66 - 4.28: 13099 4.28 - 4.90: 21920 Nonbonded interactions: 46738 Sorted by model distance: nonbonded pdb=" OD2 ASP A 652 " pdb="ZN ZN A 802 " model vdw 1.805 2.230 nonbonded pdb=" OG SER A 391 " pdb=" OAP AV0 A 801 " model vdw 2.244 3.040 nonbonded pdb=" OD2 ASP A 599 " pdb=" OG1 THR A 627 " model vdw 2.420 3.040 nonbonded pdb=" O LEU A 267 " pdb=" OG SER A 270 " model vdw 2.427 3.040 nonbonded pdb=" OE1 GLN A 369 " pdb=" CAB AV0 A 801 " model vdw 2.429 3.460 ... (remaining 46733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 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 : 0.011 0.358 5761 Z= 0.674 Angle : 1.330 7.220 7841 Z= 0.895 Chirality : 0.073 0.217 907 Planarity : 0.010 0.092 960 Dihedral : 14.363 139.056 2116 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.51 % Allowed : 3.56 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.95 (0.28), residues: 698 helix: 0.26 (0.25), residues: 335 sheet: -0.15 (0.58), residues: 55 loop : -1.72 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG A 281 TYR 0.047 0.010 TYR A 539 PHE 0.049 0.009 PHE A 57 TRP 0.060 0.010 TRP A 53 HIS 0.017 0.005 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.01006 / 0.65 ( 5758) covalent geometry : angle 1.32966 / 0.89 ( 7839) SS BOND : bond 0.06284 / 3.31 ( 1) SS BOND : angle 3.04561 / 1.77 ( 2) hydrogen bonds : bond 0.13747 / 9.08 ( 324) hydrogen bonds : angle 6.11397 / 4.22 ( 918) metal coordination : bond 0.27531 / 14.29 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.221 Fit side-chains REVERT: A 26 TYR cc_start: 0.6205 (m-10) cc_final: 0.5991 (m-10) REVERT: A 40 LYS cc_start: 0.6813 (mtmt) cc_final: 0.6378 (mtmt) REVERT: A 74 GLN cc_start: 0.8170 (tt0) cc_final: 0.7851 (tt0) REVERT: A 76 ARG cc_start: 0.7376 (ttt-90) cc_final: 0.7031 (ttt180) REVERT: A 202 GLN cc_start: 0.7023 (tt0) cc_final: 0.6573 (tp40) REVERT: A 370 TRP cc_start: 0.5141 (t60) cc_final: 0.4601 (m-10) REVERT: A 394 MET cc_start: 0.6382 (mmm) cc_final: 0.6129 (mmt) REVERT: A 411 MET cc_start: 0.6418 (mmm) cc_final: 0.6110 (mmm) REVERT: A 553 GLU cc_start: 0.7452 (tp30) cc_final: 0.6941 (tt0) REVERT: A 663 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 674 GLN cc_start: 0.8209 (mt0) cc_final: 0.7761 (mt0) REVERT: A 730 THR cc_start: 0.7801 (t) cc_final: 0.7548 (m) REVERT: A 745 ARG cc_start: 0.6237 (ttp80) cc_final: 0.5902 (mmm160) REVERT: A 747 GLU cc_start: 0.7759 (tt0) cc_final: 0.7137 (tm-30) outliers start: 3 outliers final: 4 residues processed: 86 average time/residue: 0.5151 time to fit residues: 46.5743 Evaluate side-chains 67 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 555 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 616 GLN A 617 GLN ** A 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124635 restraints weight = 6000.067| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.63 r_work: 0.3295 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5761 Z= 0.137 Angle : 0.571 6.255 7841 Z= 0.290 Chirality : 0.039 0.146 907 Planarity : 0.004 0.033 960 Dihedral : 11.302 147.762 885 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.86 % Allowed : 7.46 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.77 (0.31), residues: 698 helix: 2.13 (0.27), residues: 339 sheet: -0.21 (0.51), residues: 70 loop : -1.35 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 245 TYR 0.012 0.001 TYR A 591 PHE 0.014 0.001 PHE A 127 TRP 0.013 0.001 TRP A 125 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 5758) covalent geometry : angle 0.57072 / 0.29 ( 7839) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 1.18165 / 0.64 ( 2) hydrogen bonds : bond 0.04301 / 2.76 ( 324) hydrogen bonds : angle 4.68783 / 3.23 ( 918) metal coordination : bond 0.01036 / 0.52 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7635 (mtpt) REVERT: A 730 THR cc_start: 0.9053 (t) cc_final: 0.8748 (m) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.5707 time to fit residues: 45.9459 Evaluate side-chains 65 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 740 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 152 GLN A 425 GLN A 645 HIS A 680 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.153898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121993 restraints weight = 6054.449| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.61 r_work: 0.3257 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5761 Z= 0.169 Angle : 0.595 5.971 7841 Z= 0.298 Chirality : 0.040 0.172 907 Planarity : 0.004 0.036 960 Dihedral : 11.353 150.497 880 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.20 % Allowed : 10.34 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.11 (0.32), residues: 698 helix: 2.49 (0.27), residues: 338 sheet: -0.26 (0.51), residues: 85 loop : -1.26 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 76 TYR 0.012 0.002 TYR A 591 PHE 0.015 0.002 PHE A 741 TRP 0.012 0.001 TRP A 125 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 5758) covalent geometry : angle 0.59458 / 0.30 ( 7839) SS BOND : bond 0.00041 / 0.02 ( 1) SS BOND : angle 1.39480 / 0.74 ( 2) hydrogen bonds : bond 0.04334 / 2.78 ( 324) hydrogen bonds : angle 4.66599 / 3.23 ( 918) metal coordination : bond 0.00358 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.215 Fit side-chains REVERT: A 40 LYS cc_start: 0.7849 (mtmt) cc_final: 0.7586 (mppt) REVERT: A 304 ARG cc_start: 0.7938 (mpp80) cc_final: 0.7693 (mpp80) REVERT: A 394 MET cc_start: 0.7233 (mmm) cc_final: 0.6888 (mmt) REVERT: A 730 THR cc_start: 0.9137 (t) cc_final: 0.8817 (m) REVERT: A 773 GLU cc_start: 0.6998 (pt0) cc_final: 0.6408 (pm20) outliers start: 13 outliers final: 7 residues processed: 74 average time/residue: 0.4866 time to fit residues: 38.0479 Evaluate side-chains 68 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 740 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.0170 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 HIS A 680 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121648 restraints weight = 6148.356| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.62 r_work: 0.3281 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5761 Z= 0.124 Angle : 0.537 5.958 7841 Z= 0.269 Chirality : 0.039 0.137 907 Planarity : 0.004 0.036 960 Dihedral : 11.292 154.275 880 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.03 % Allowed : 11.53 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.33 (0.32), residues: 698 helix: 2.76 (0.27), residues: 338 sheet: -0.30 (0.53), residues: 81 loop : -1.21 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 534 TYR 0.009 0.001 TYR A 591 PHE 0.011 0.001 PHE A 741 TRP 0.011 0.001 TRP A 125 HIS 0.005 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 5758) covalent geometry : angle 0.53718 / 0.27 ( 7839) SS BOND : bond 0.00080 / 0.04 ( 1) SS BOND : angle 1.12859 / 0.60 ( 2) hydrogen bonds : bond 0.03771 / 2.41 ( 324) hydrogen bonds : angle 4.52355 / 3.14 ( 918) metal coordination : bond 0.00133 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.221 Fit side-chains REVERT: A 35 LEU cc_start: 0.8640 (mp) cc_final: 0.8378 (mm) REVERT: A 40 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7383 (mmpt) REVERT: A 394 MET cc_start: 0.7251 (mmm) cc_final: 0.6807 (mmt) REVERT: A 730 THR cc_start: 0.9117 (t) cc_final: 0.8777 (m) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.5244 time to fit residues: 38.6200 Evaluate side-chains 62 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 740 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120702 restraints weight = 6276.103| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.69 r_work: 0.3194 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5761 Z= 0.126 Angle : 0.543 7.997 7841 Z= 0.268 Chirality : 0.039 0.140 907 Planarity : 0.004 0.038 960 Dihedral : 11.258 156.226 880 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.37 % Allowed : 11.86 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.44 (0.33), residues: 698 helix: 2.85 (0.27), residues: 338 sheet: -0.23 (0.55), residues: 81 loop : -1.15 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.023 0.001 TYR A 236 PHE 0.012 0.001 PHE A 741 TRP 0.011 0.001 TRP A 125 HIS 0.005 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5758) covalent geometry : angle 0.54253 / 0.27 ( 7839) SS BOND : bond 0.00076 / 0.04 ( 1) SS BOND : angle 1.17504 / 0.63 ( 2) hydrogen bonds : bond 0.03703 / 2.36 ( 324) hydrogen bonds : angle 4.47775 / 3.10 ( 918) metal coordination : bond 0.00160 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.230 Fit side-chains REVERT: A 35 LEU cc_start: 0.8604 (mp) cc_final: 0.8336 (mm) REVERT: A 40 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7330 (mmpt) REVERT: A 394 MET cc_start: 0.7122 (mmm) cc_final: 0.6662 (mmt) REVERT: A 654 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: A 730 THR cc_start: 0.9108 (t) cc_final: 0.8773 (m) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.4678 time to fit residues: 33.2623 Evaluate side-chains 65 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 0.0040 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121712 restraints weight = 6237.903| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.71 r_work: 0.3211 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5761 Z= 0.117 Angle : 0.528 8.231 7841 Z= 0.260 Chirality : 0.038 0.131 907 Planarity : 0.004 0.037 960 Dihedral : 11.221 158.889 880 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.71 % Allowed : 11.69 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.57 (0.33), residues: 698 helix: 2.96 (0.28), residues: 338 sheet: -0.14 (0.56), residues: 81 loop : -1.12 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.008 0.001 TYR A 591 PHE 0.011 0.001 PHE A 741 TRP 0.014 0.001 TRP A 370 HIS 0.004 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 5758) covalent geometry : angle 0.52758 / 0.26 ( 7839) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 1.04877 / 0.56 ( 2) hydrogen bonds : bond 0.03551 / 2.26 ( 324) hydrogen bonds : angle 4.43082 / 3.07 ( 918) metal coordination : bond 0.00124 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.205 Fit side-chains REVERT: A 35 LEU cc_start: 0.8567 (mp) cc_final: 0.8305 (mm) REVERT: A 40 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7345 (mmpt) REVERT: A 394 MET cc_start: 0.7064 (mmm) cc_final: 0.6614 (mmt) REVERT: A 654 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8160 (mm-30) REVERT: A 730 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8794 (m) REVERT: A 745 ARG cc_start: 0.6983 (ptt90) cc_final: 0.6756 (ptm160) outliers start: 16 outliers final: 9 residues processed: 69 average time/residue: 0.5011 time to fit residues: 36.4329 Evaluate side-chains 67 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 740 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 0.0070 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121892 restraints weight = 6364.487| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.72 r_work: 0.3211 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5761 Z= 0.112 Angle : 0.512 5.476 7841 Z= 0.256 Chirality : 0.038 0.128 907 Planarity : 0.004 0.037 960 Dihedral : 11.216 160.269 880 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.05 % Allowed : 12.20 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.64 (0.33), residues: 698 helix: 3.00 (0.28), residues: 338 sheet: -0.09 (0.57), residues: 81 loop : -1.06 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 76 TYR 0.008 0.001 TYR A 710 PHE 0.011 0.001 PHE A 365 TRP 0.016 0.001 TRP A 370 HIS 0.004 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 5758) covalent geometry : angle 0.51170 / 0.26 ( 7839) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 1.01834 / 0.54 ( 2) hydrogen bonds : bond 0.03459 / 2.20 ( 324) hydrogen bonds : angle 4.39041 / 3.04 ( 918) metal coordination : bond 0.00128 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.214 Fit side-chains REVERT: A 40 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7344 (mmpt) REVERT: A 394 MET cc_start: 0.7040 (mmm) cc_final: 0.6597 (mmt) REVERT: A 666 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7436 (tm) REVERT: A 730 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8794 (m) outliers start: 18 outliers final: 11 residues processed: 70 average time/residue: 0.4512 time to fit residues: 33.5803 Evaluate side-chains 70 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 740 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119725 restraints weight = 6262.792| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.71 r_work: 0.3164 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5761 Z= 0.148 Angle : 0.557 5.563 7841 Z= 0.278 Chirality : 0.039 0.154 907 Planarity : 0.004 0.037 960 Dihedral : 11.366 159.089 880 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.88 % Allowed : 12.54 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.48 (0.33), residues: 698 helix: 2.84 (0.27), residues: 339 sheet: -0.16 (0.57), residues: 81 loop : -1.11 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.009 0.001 TYR A 591 PHE 0.013 0.001 PHE A 741 TRP 0.017 0.001 TRP A 370 HIS 0.005 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 5758) covalent geometry : angle 0.55568 / 0.28 ( 7839) SS BOND : bond 0.00045 / 0.02 ( 1) SS BOND : angle 2.69681 / 1.47 ( 2) hydrogen bonds : bond 0.03823 / 2.45 ( 324) hydrogen bonds : angle 4.50468 / 3.11 ( 918) metal coordination : bond 0.00248 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.228 Fit side-chains REVERT: A 40 LYS cc_start: 0.7875 (mtmt) cc_final: 0.7376 (mmpt) REVERT: A 394 MET cc_start: 0.7239 (mmm) cc_final: 0.6768 (mmt) REVERT: A 666 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7483 (tm) REVERT: A 730 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8773 (m) outliers start: 17 outliers final: 12 residues processed: 66 average time/residue: 0.4159 time to fit residues: 29.3001 Evaluate side-chains 69 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 740 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 HIS A 771 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121187 restraints weight = 6317.694| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.72 r_work: 0.3206 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5761 Z= 0.122 Angle : 0.526 5.500 7841 Z= 0.263 Chirality : 0.038 0.133 907 Planarity : 0.004 0.036 960 Dihedral : 11.375 162.828 880 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.88 % Allowed : 12.88 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.57 (0.33), residues: 698 helix: 2.94 (0.28), residues: 338 sheet: -0.12 (0.57), residues: 81 loop : -1.08 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.008 0.001 TYR A 271 PHE 0.011 0.001 PHE A 741 TRP 0.018 0.001 TRP A 370 HIS 0.004 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 5758) covalent geometry : angle 0.52453 / 0.26 ( 7839) SS BOND : bond 0.00173 / 0.09 ( 1) SS BOND : angle 2.61517 / 1.44 ( 2) hydrogen bonds : bond 0.03543 / 2.26 ( 324) hydrogen bonds : angle 4.43402 / 3.07 ( 918) metal coordination : bond 0.00149 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.203 Fit side-chains REVERT: A 40 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7368 (mmpt) REVERT: A 245 ARG cc_start: 0.7268 (ttp80) cc_final: 0.7050 (tmm160) REVERT: A 394 MET cc_start: 0.7041 (mmm) cc_final: 0.6577 (mmt) REVERT: A 666 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7512 (tm) REVERT: A 730 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8784 (m) outliers start: 17 outliers final: 12 residues processed: 66 average time/residue: 0.4460 time to fit residues: 31.3886 Evaluate side-chains 68 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 740 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.153955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121111 restraints weight = 6386.845| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.73 r_work: 0.3206 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5761 Z= 0.119 Angle : 0.521 5.498 7841 Z= 0.261 Chirality : 0.038 0.135 907 Planarity : 0.004 0.036 960 Dihedral : 10.882 166.628 880 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.88 % Allowed : 13.22 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.63 (0.33), residues: 698 helix: 2.98 (0.28), residues: 338 sheet: -0.09 (0.56), residues: 81 loop : -1.05 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.008 0.001 TYR A 591 PHE 0.011 0.001 PHE A 741 TRP 0.020 0.001 TRP A 370 HIS 0.004 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 5758) covalent geometry : angle 0.52028 / 0.26 ( 7839) SS BOND : bond 0.00097 / 0.05 ( 1) SS BOND : angle 2.03360 / 1.12 ( 2) hydrogen bonds : bond 0.03503 / 2.24 ( 324) hydrogen bonds : angle 4.41102 / 3.05 ( 918) metal coordination : bond 0.00161 / 0.08 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.226 Fit side-chains REVERT: A 35 LEU cc_start: 0.8601 (mp) cc_final: 0.8052 (tp) REVERT: A 40 LYS cc_start: 0.7872 (mtmt) cc_final: 0.7380 (mmpt) REVERT: A 394 MET cc_start: 0.7175 (mmm) cc_final: 0.6733 (mmt) REVERT: A 666 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7508 (tm) REVERT: A 730 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8777 (m) outliers start: 17 outliers final: 12 residues processed: 67 average time/residue: 0.3841 time to fit residues: 27.6042 Evaluate side-chains 69 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 740 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.152845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120139 restraints weight = 6274.213| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.71 r_work: 0.3188 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5761 Z= 0.138 Angle : 0.544 5.555 7841 Z= 0.272 Chirality : 0.039 0.149 907 Planarity : 0.004 0.036 960 Dihedral : 10.792 164.885 880 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.71 % Allowed : 13.22 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.33), residues: 698 helix: 2.85 (0.27), residues: 339 sheet: -0.14 (0.56), residues: 81 loop : -1.08 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.023 0.002 TYR A 236 PHE 0.013 0.001 PHE A 741 TRP 0.020 0.001 TRP A 370 HIS 0.004 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 5758) covalent geometry : angle 0.54296 / 0.27 ( 7839) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 2.20031 / 1.22 ( 2) hydrogen bonds : bond 0.03721 / 2.39 ( 324) hydrogen bonds : angle 4.48572 / 3.11 ( 918) metal coordination : bond 0.00208 / 0.11 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.13 seconds wall clock time: 37 minutes 43.11 seconds (2263.11 seconds total)