Starting phenix.real_space_refine on Tue Aug 4 15:41:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13bs_76948/08_2026/13bs_76948.cif Found real_map, /net/cci-nas-00/data/ceres_data/13bs_76948/08_2026/13bs_76948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13bs_76948/08_2026/13bs_76948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13bs_76948/08_2026/13bs_76948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13bs_76948/08_2026/13bs_76948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13bs_76948/08_2026/13bs_76948.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2768 2.51 5 N 739 2.21 5 O 868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4396 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1115 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 9, 'TRANS': 135} Chain breaks: 1 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1658 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 210} Chain: "L" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1623 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 0.82, per 1000 atoms: 0.19 Number of scatterers: 4396 At special positions: 0 Unit cell: (74.56, 93.2, 93.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 868 8.00 N 739 7.00 C 2768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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: 0.23 Conformation dependent library (CDL) restraints added in 151.8 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 14 sheets defined 9.3% alpha, 49.4% 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 30 through 34 removed outlier: 3.824A pdb=" N GLY A 34 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 54 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.794A pdb=" N SER A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.731A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 removed outlier: 3.675A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 31' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.929A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.045A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.514A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.421A pdb=" N LEU A 59 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N CYS A 70 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 14.002A pdb=" N VAL A 57 " --> pdb=" O CYS A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.421A pdb=" N LEU A 59 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N CYS A 70 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 14.002A pdb=" N VAL A 57 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 7 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 21 removed outlier: 6.568A pdb=" N LEU A 26 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN A 129 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.715A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.715A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 125 through 129 removed outlier: 6.004A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 125 through 129 removed outlier: 6.004A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.296A pdb=" N TYR H 199 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.974A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.795A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.574A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.857A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.810A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 522 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: 0.49 Time building geometry restraints manager: 0.31 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: 1415 1.34 - 1.47: 1110 1.47 - 1.59: 1942 1.59 - 1.71: 0 1.71 - 1.83: 27 Bond restraints: 4494 Sorted by residual: bond pdb=" N ILE A 144 " pdb=" CA ILE A 144 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.11e-02 8.12e+03 8.35e+00 bond pdb=" C LEU L 78 " pdb=" N GLU L 79 " ideal model delta sigma weight residual 1.329 1.296 0.033 1.86e-02 2.89e+03 3.18e+00 bond pdb=" N PRO A 143 " pdb=" CD PRO A 143 " ideal model delta sigma weight residual 1.473 1.496 -0.023 1.40e-02 5.10e+03 2.81e+00 bond pdb=" CA THR A 134 " pdb=" C THR A 134 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.24e-02 6.50e+03 2.53e+00 bond pdb=" N LEU A 136 " pdb=" CA LEU A 136 " ideal model delta sigma weight residual 1.454 1.474 -0.020 1.29e-02 6.01e+03 2.51e+00 ... (remaining 4489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 5998 2.35 - 4.70: 88 4.70 - 7.05: 13 7.05 - 9.40: 5 9.40 - 11.76: 1 Bond angle restraints: 6105 Sorted by residual: angle pdb=" C ASP A 146 " pdb=" N PHE A 147 " pdb=" CA PHE A 147 " ideal model delta sigma weight residual 120.94 132.70 -11.76 1.57e+00 4.06e-01 5.61e+01 angle pdb=" N GLN A 135 " pdb=" CA GLN A 135 " pdb=" C GLN A 135 " ideal model delta sigma weight residual 109.07 100.07 9.00 1.61e+00 3.86e-01 3.13e+01 angle pdb=" N THR A 145 " pdb=" CA THR A 145 " pdb=" C THR A 145 " ideal model delta sigma weight residual 109.23 116.75 -7.52 1.55e+00 4.16e-01 2.35e+01 angle pdb=" C ILE A 144 " pdb=" N THR A 145 " pdb=" CA THR A 145 " ideal model delta sigma weight residual 122.29 114.80 7.49 1.65e+00 3.67e-01 2.06e+01 angle pdb=" C PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta sigma weight residual 110.10 117.97 -7.87 1.90e+00 2.77e-01 1.71e+01 ... (remaining 6100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 2352 17.72 - 35.44: 226 35.44 - 53.16: 85 53.16 - 70.88: 21 70.88 - 88.60: 3 Dihedral angle restraints: 2687 sinusoidal: 1028 harmonic: 1659 Sorted by residual: dihedral pdb=" CB CYS A 8 " pdb=" SG CYS A 8 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 31.81 61.19 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CA GLU H 153 " pdb=" C GLU H 153 " pdb=" N PRO H 154 " pdb=" CA PRO H 154 " ideal model delta harmonic sigma weight residual 180.00 149.42 30.58 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" C GLN A 135 " pdb=" N GLN A 135 " pdb=" CA GLN A 135 " pdb=" CB GLN A 135 " ideal model delta harmonic sigma weight residual -122.60 -111.00 -11.60 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 2684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 600 0.067 - 0.133: 82 0.133 - 0.200: 4 0.200 - 0.267: 0 0.267 - 0.333: 2 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA GLN A 135 " pdb=" N GLN A 135 " pdb=" C GLN A 135 " pdb=" CB GLN A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA THR A 145 " pdb=" N THR A 145 " pdb=" C THR A 145 " pdb=" CB THR A 145 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ILE A 144 " pdb=" N ILE A 144 " pdb=" C ILE A 144 " pdb=" CB ILE A 144 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 685 not shown) Planarity restraints: 783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 153 " 0.083 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO H 154 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO H 154 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO H 154 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 133 " 0.022 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C LEU A 133 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU A 133 " 0.031 2.00e-02 2.50e+03 pdb=" N THR A 134 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 146 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C ASP A 146 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP A 146 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE A 147 " -0.012 2.00e-02 2.50e+03 ... (remaining 780 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 55 2.65 - 3.22: 3620 3.22 - 3.78: 6429 3.78 - 4.34: 9259 4.34 - 4.90: 15632 Nonbonded interactions: 34995 Sorted by model distance: nonbonded pdb=" ND2 ASN H 202 " pdb=" OD1 ASP H 213 " model vdw 2.094 3.120 nonbonded pdb=" OG SER H 208 " pdb=" OG1 THR H 210 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP H 73 " pdb=" OG1 THR H 76 " model vdw 2.288 3.040 nonbonded pdb=" OE1 GLU L 105 " pdb=" OH TYR L 173 " model vdw 2.297 3.040 nonbonded pdb=" NH1 ARG A 48 " pdb=" OD2 ASP H 99 " model vdw 2.302 3.120 ... (remaining 34990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.880 Find NCS groups from input model: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4499 Z= 0.188 Angle : 0.737 11.755 6115 Z= 0.418 Chirality : 0.047 0.333 688 Planarity : 0.007 0.128 783 Dihedral : 16.845 88.600 1614 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.83 % Allowed : 18.33 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.14 (0.35), residues: 573 helix: 0.87 (1.25), residues: 21 sheet: 1.00 (0.30), residues: 268 loop : 0.65 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.013 0.001 TYR H 60 PHE 0.012 0.001 PHE A 149 TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 ( 4494) covalent geometry : angle 0.73327 / 0.42 ( 6105) SS BOND : bond 0.00332 / 0.17 ( 5) SS BOND : angle 1.88201 / 0.97 ( 10) hydrogen bonds : bond 0.12089 / 7.50 ( 174) hydrogen bonds : angle 6.24481 / 4.14 ( 522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.171 Fit side-chains REVERT: A 105 MET cc_start: 0.7244 (mtt) cc_final: 0.6464 (mmt) REVERT: H 158 SER cc_start: 0.8319 (m) cc_final: 0.7967 (p) REVERT: H 202 ASN cc_start: 0.8412 (m110) cc_final: 0.8163 (m110) REVERT: H 211 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7758 (mtmt) REVERT: H 215 LYS cc_start: 0.8743 (tttt) cc_final: 0.8474 (tttm) REVERT: L 18 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.8055 (mtp85) REVERT: L 42 GLN cc_start: 0.8250 (tt0) cc_final: 0.7940 (mt0) REVERT: L 79 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7686 (mm-30) REVERT: L 147 GLN cc_start: 0.7989 (mt0) cc_final: 0.7384 (mt0) REVERT: L 185 ASP cc_start: 0.8066 (m-30) cc_final: 0.7865 (t0) outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 0.0648 time to fit residues: 8.9806 Evaluate side-chains 78 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 143 PRO Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 66 GLN H 43 GLN H 59 ASN H 204 ASN L 6 GLN L 124 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.130546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.094382 restraints weight = 5180.115| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.11 r_work: 0.2960 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4499 Z= 0.127 Angle : 0.594 8.292 6115 Z= 0.298 Chirality : 0.043 0.171 688 Planarity : 0.006 0.090 783 Dihedral : 5.718 59.760 631 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.05 % Allowed : 16.70 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.27 (0.36), residues: 573 helix: 0.39 (1.12), residues: 22 sheet: 1.12 (0.31), residues: 266 loop : 0.76 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.006 0.001 TYR L 49 PHE 0.012 0.001 PHE A 149 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4494) covalent geometry : angle 0.59073 / 0.30 ( 6105) SS BOND : bond 0.00220 / 0.11 ( 5) SS BOND : angle 1.73910 / 0.90 ( 10) hydrogen bonds : bond 0.03273 / 2.18 ( 174) hydrogen bonds : angle 5.05625 / 3.44 ( 522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.097 Fit side-chains REVERT: A 105 MET cc_start: 0.7147 (mtt) cc_final: 0.6288 (mmt) REVERT: H 84 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7985 (mtm110) REVERT: H 96 CYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7687 (p) REVERT: H 202 ASN cc_start: 0.8513 (m110) cc_final: 0.8173 (m110) REVERT: H 204 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8318 (t0) REVERT: L 18 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.8141 (mtp85) REVERT: L 79 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8097 (mm-30) outliers start: 15 outliers final: 6 residues processed: 80 average time/residue: 0.0453 time to fit residues: 4.6725 Evaluate side-chains 66 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 203 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN H 43 GLN H 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.085511 restraints weight = 5202.787| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.12 r_work: 0.2683 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 4499 Z= 0.286 Angle : 0.688 7.773 6115 Z= 0.351 Chirality : 0.046 0.177 688 Planarity : 0.006 0.088 783 Dihedral : 5.146 30.907 621 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.87 % Allowed : 17.92 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.23 (0.36), residues: 573 helix: 0.28 (1.10), residues: 22 sheet: 1.30 (0.32), residues: 248 loop : 0.55 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 87 TYR 0.012 0.002 TYR L 140 PHE 0.016 0.002 PHE L 83 TRP 0.012 0.002 TRP H 50 HIS 0.006 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.29 ( 4494) covalent geometry : angle 0.68337 / 0.35 ( 6105) SS BOND : bond 0.00480 / 0.24 ( 5) SS BOND : angle 2.08404 / 1.06 ( 10) hydrogen bonds : bond 0.03832 / 2.45 ( 174) hydrogen bonds : angle 5.56827 / 3.83 ( 522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.095 Fit side-chains REVERT: A 105 MET cc_start: 0.7286 (mtt) cc_final: 0.6457 (mmt) REVERT: A 122 CYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7738 (p) REVERT: A 147 PHE cc_start: 0.8386 (m-80) cc_final: 0.7812 (m-80) REVERT: H 69 THR cc_start: 0.8689 (m) cc_final: 0.8222 (p) REVERT: H 82 GLU cc_start: 0.7921 (tt0) cc_final: 0.7139 (tm-30) REVERT: H 96 CYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8418 (p) REVERT: L 1 GLU cc_start: 0.7424 (tt0) cc_final: 0.6992 (tt0) REVERT: L 18 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.8106 (ttm-80) REVERT: L 24 ARG cc_start: 0.8316 (ttm170) cc_final: 0.7942 (ttm-80) REVERT: L 79 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8020 (mm-30) REVERT: L 188 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7833 (ttmt) outliers start: 19 outliers final: 12 residues processed: 76 average time/residue: 0.0623 time to fit residues: 5.7831 Evaluate side-chains 69 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.124718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.089186 restraints weight = 5098.018| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.06 r_work: 0.2872 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4499 Z= 0.139 Angle : 0.559 5.975 6115 Z= 0.283 Chirality : 0.042 0.144 688 Planarity : 0.005 0.072 783 Dihedral : 4.583 29.613 621 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.48 % Allowed : 17.52 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: 1.27 (0.36), residues: 573 helix: 0.21 (1.12), residues: 23 sheet: 1.34 (0.32), residues: 251 loop : 0.57 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 142 TYR 0.012 0.001 TYR A 116 PHE 0.010 0.001 PHE L 139 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 4494) covalent geometry : angle 0.55600 / 0.28 ( 6105) SS BOND : bond 0.00308 / 0.16 ( 5) SS BOND : angle 1.50006 / 0.77 ( 10) hydrogen bonds : bond 0.03090 / 2.01 ( 174) hydrogen bonds : angle 5.06563 / 3.48 ( 522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.132 Fit side-chains REVERT: A 87 GLU cc_start: 0.6646 (mp0) cc_final: 0.6373 (mp0) REVERT: A 105 MET cc_start: 0.7329 (mtt) cc_final: 0.6558 (mmt) REVERT: A 147 PHE cc_start: 0.8522 (m-80) cc_final: 0.7956 (m-80) REVERT: H 63 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7977 (ptmt) REVERT: H 69 THR cc_start: 0.8687 (m) cc_final: 0.8246 (p) REVERT: H 73 ASP cc_start: 0.7581 (t70) cc_final: 0.7178 (t0) REVERT: H 82 GLU cc_start: 0.7922 (tt0) cc_final: 0.7218 (tm-30) REVERT: H 158 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8482 (p) REVERT: L 1 GLU cc_start: 0.7377 (tt0) cc_final: 0.6823 (tt0) REVERT: L 18 ARG cc_start: 0.8428 (mtp-110) cc_final: 0.8186 (ttm170) REVERT: L 24 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7837 (ttm-80) REVERT: L 79 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8027 (mm-30) REVERT: L 188 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7870 (ttmt) outliers start: 22 outliers final: 14 residues processed: 78 average time/residue: 0.0732 time to fit residues: 7.1475 Evaluate side-chains 71 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.089458 restraints weight = 5132.535| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.06 r_work: 0.2881 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4499 Z= 0.126 Angle : 0.549 6.753 6115 Z= 0.278 Chirality : 0.042 0.165 688 Planarity : 0.005 0.070 783 Dihedral : 4.486 29.791 621 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.46 % Allowed : 19.14 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: 1.37 (0.36), residues: 573 helix: 0.47 (1.13), residues: 23 sheet: 1.37 (0.32), residues: 252 loop : 0.66 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 142 TYR 0.010 0.001 TYR A 116 PHE 0.010 0.001 PHE L 139 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4494) covalent geometry : angle 0.54675 / 0.28 ( 6105) SS BOND : bond 0.00348 / 0.17 ( 5) SS BOND : angle 1.42352 / 0.73 ( 10) hydrogen bonds : bond 0.02911 / 1.88 ( 174) hydrogen bonds : angle 4.94502 / 3.40 ( 522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.096 Fit side-chains REVERT: A 105 MET cc_start: 0.7262 (mtt) cc_final: 0.6489 (mmt) REVERT: A 109 SER cc_start: 0.9066 (m) cc_final: 0.8415 (p) REVERT: A 147 PHE cc_start: 0.8541 (m-80) cc_final: 0.7796 (m-80) REVERT: H 63 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7918 (ptmt) REVERT: H 69 THR cc_start: 0.8681 (m) cc_final: 0.8230 (p) REVERT: H 73 ASP cc_start: 0.7536 (t70) cc_final: 0.7143 (t0) REVERT: H 82 GLU cc_start: 0.7867 (tt0) cc_final: 0.7165 (tm-30) REVERT: H 158 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8481 (p) REVERT: L 1 GLU cc_start: 0.7380 (tt0) cc_final: 0.7166 (tt0) REVERT: L 18 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.8146 (ttm-80) REVERT: L 24 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7802 (ttm-80) REVERT: L 79 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7943 (mm-30) REVERT: L 188 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7777 (ttmt) outliers start: 17 outliers final: 14 residues processed: 72 average time/residue: 0.0607 time to fit residues: 5.5418 Evaluate side-chains 73 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 0.0270 overall best weight: 0.9642 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.123928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.087902 restraints weight = 5268.281| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.11 r_work: 0.2870 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4499 Z= 0.157 Angle : 0.570 6.956 6115 Z= 0.288 Chirality : 0.042 0.173 688 Planarity : 0.005 0.070 783 Dihedral : 4.592 29.943 621 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.67 % Allowed : 19.35 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: 1.31 (0.36), residues: 573 helix: 0.26 (1.09), residues: 23 sheet: 1.26 (0.32), residues: 259 loop : 0.69 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.010 0.001 TYR A 116 PHE 0.011 0.001 PHE L 83 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 4494) covalent geometry : angle 0.56689 / 0.29 ( 6105) SS BOND : bond 0.00307 / 0.15 ( 5) SS BOND : angle 1.51816 / 0.78 ( 10) hydrogen bonds : bond 0.02998 / 1.93 ( 174) hydrogen bonds : angle 5.00528 / 3.44 ( 522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.160 Fit side-chains REVERT: A 105 MET cc_start: 0.7318 (mtt) cc_final: 0.6574 (mmt) REVERT: A 109 SER cc_start: 0.9080 (m) cc_final: 0.8409 (p) REVERT: A 122 CYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7693 (p) REVERT: A 147 PHE cc_start: 0.8570 (m-80) cc_final: 0.7974 (m-80) REVERT: H 69 THR cc_start: 0.8688 (m) cc_final: 0.8253 (p) REVERT: H 73 ASP cc_start: 0.7603 (t70) cc_final: 0.7170 (t0) REVERT: H 158 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8428 (p) REVERT: L 24 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7815 (ttm-80) REVERT: L 188 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7765 (ttmt) outliers start: 18 outliers final: 14 residues processed: 64 average time/residue: 0.0797 time to fit residues: 6.4043 Evaluate side-chains 69 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.124589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.088925 restraints weight = 5191.778| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.09 r_work: 0.2735 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4499 Z= 0.128 Angle : 0.544 6.328 6115 Z= 0.274 Chirality : 0.042 0.166 688 Planarity : 0.005 0.067 783 Dihedral : 4.457 29.847 621 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.67 % Allowed : 20.57 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: 1.34 (0.36), residues: 573 helix: 0.35 (1.09), residues: 23 sheet: 1.36 (0.32), residues: 252 loop : 0.64 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.010 0.001 TYR A 116 PHE 0.010 0.001 PHE L 139 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 4494) covalent geometry : angle 0.54193 / 0.27 ( 6105) SS BOND : bond 0.00282 / 0.14 ( 5) SS BOND : angle 1.29255 / 0.67 ( 10) hydrogen bonds : bond 0.02853 / 1.83 ( 174) hydrogen bonds : angle 4.88060 / 3.35 ( 522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.157 Fit side-chains REVERT: A 105 MET cc_start: 0.7298 (mtt) cc_final: 0.6500 (mmt) REVERT: A 109 SER cc_start: 0.9052 (m) cc_final: 0.8376 (p) REVERT: A 147 PHE cc_start: 0.8514 (m-80) cc_final: 0.7939 (m-80) REVERT: H 63 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7869 (ptmt) REVERT: H 69 THR cc_start: 0.8692 (m) cc_final: 0.8234 (p) REVERT: H 82 GLU cc_start: 0.7842 (tt0) cc_final: 0.7421 (tt0) REVERT: H 158 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8364 (p) REVERT: L 24 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7757 (ttm-80) REVERT: L 188 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7732 (ttmt) outliers start: 18 outliers final: 17 residues processed: 63 average time/residue: 0.0724 time to fit residues: 5.8090 Evaluate side-chains 68 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 56 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.6008 > 50:) chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.123751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.088084 restraints weight = 5195.818| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.08 r_work: 0.2873 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4499 Z= 0.156 Angle : 0.562 6.686 6115 Z= 0.282 Chirality : 0.042 0.173 688 Planarity : 0.005 0.070 783 Dihedral : 4.547 30.253 621 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.28 % Allowed : 19.76 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.30 (0.36), residues: 573 helix: 0.22 (1.06), residues: 23 sheet: 1.28 (0.32), residues: 259 loop : 0.65 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 142 TYR 0.010 0.001 TYR A 116 PHE 0.010 0.001 PHE L 83 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 4494) covalent geometry : angle 0.55969 / 0.28 ( 6105) SS BOND : bond 0.00329 / 0.17 ( 5) SS BOND : angle 1.36821 / 0.71 ( 10) hydrogen bonds : bond 0.02937 / 1.88 ( 174) hydrogen bonds : angle 4.96849 / 3.41 ( 522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.095 Fit side-chains REVERT: A 105 MET cc_start: 0.7338 (mtt) cc_final: 0.6541 (mmt) REVERT: A 109 SER cc_start: 0.9116 (m) cc_final: 0.8401 (p) REVERT: A 122 CYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7680 (p) REVERT: A 147 PHE cc_start: 0.8540 (m-80) cc_final: 0.8001 (m-80) REVERT: H 69 THR cc_start: 0.8687 (m) cc_final: 0.8271 (p) REVERT: H 73 ASP cc_start: 0.7511 (t0) cc_final: 0.7230 (t0) REVERT: H 82 GLU cc_start: 0.7825 (tt0) cc_final: 0.7445 (tt0) REVERT: H 158 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8382 (p) REVERT: L 24 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7813 (ttm-80) REVERT: L 188 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7760 (ttmt) outliers start: 21 outliers final: 17 residues processed: 65 average time/residue: 0.0526 time to fit residues: 4.3578 Evaluate side-chains 71 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.122362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.086527 restraints weight = 5235.191| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.09 r_work: 0.2850 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 4499 Z= 0.194 Angle : 0.591 7.308 6115 Z= 0.298 Chirality : 0.043 0.182 688 Planarity : 0.005 0.070 783 Dihedral : 4.710 30.892 621 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.28 % Allowed : 20.16 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.22 (0.36), residues: 573 helix: 0.11 (1.04), residues: 23 sheet: 1.25 (0.32), residues: 257 loop : 0.58 (0.39), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.010 0.002 TYR A 116 PHE 0.012 0.002 PHE L 83 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.19 ( 4494) covalent geometry : angle 0.58791 / 0.30 ( 6105) SS BOND : bond 0.00380 / 0.19 ( 5) SS BOND : angle 1.53571 / 0.80 ( 10) hydrogen bonds : bond 0.03110 / 1.99 ( 174) hydrogen bonds : angle 5.10436 / 3.50 ( 522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.7389 (mtt) cc_final: 0.6643 (mmt) REVERT: A 109 SER cc_start: 0.9127 (m) cc_final: 0.8386 (p) REVERT: A 122 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7769 (p) REVERT: A 147 PHE cc_start: 0.8558 (m-80) cc_final: 0.8023 (m-80) REVERT: H 63 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7852 (ptmt) REVERT: H 82 GLU cc_start: 0.7901 (tt0) cc_final: 0.7619 (tt0) REVERT: H 158 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8306 (p) REVERT: L 188 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7754 (ttmt) outliers start: 21 outliers final: 17 residues processed: 65 average time/residue: 0.0768 time to fit residues: 6.1595 Evaluate side-chains 69 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.123844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.088139 restraints weight = 5208.169| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.10 r_work: 0.2843 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4499 Z= 0.137 Angle : 0.555 6.609 6115 Z= 0.280 Chirality : 0.042 0.177 688 Planarity : 0.005 0.068 783 Dihedral : 4.521 30.055 621 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.07 % Allowed : 20.57 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.26 (0.36), residues: 573 helix: 0.34 (1.08), residues: 23 sheet: 1.37 (0.32), residues: 252 loop : 0.51 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 142 TYR 0.011 0.001 TYR A 116 PHE 0.009 0.001 PHE L 139 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4494) covalent geometry : angle 0.55276 / 0.28 ( 6105) SS BOND : bond 0.00292 / 0.15 ( 5) SS BOND : angle 1.26360 / 0.66 ( 10) hydrogen bonds : bond 0.02871 / 1.84 ( 174) hydrogen bonds : angle 4.90228 / 3.36 ( 522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.103 Fit side-chains REVERT: A 105 MET cc_start: 0.7300 (mtt) cc_final: 0.6553 (mmt) REVERT: A 109 SER cc_start: 0.9104 (m) cc_final: 0.8395 (p) REVERT: A 122 CYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7797 (p) REVERT: A 147 PHE cc_start: 0.8526 (m-80) cc_final: 0.7984 (m-80) REVERT: H 63 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7968 (ptmt) REVERT: H 69 THR cc_start: 0.8700 (m) cc_final: 0.8279 (p) REVERT: H 73 ASP cc_start: 0.7346 (t0) cc_final: 0.7122 (t0) REVERT: H 82 GLU cc_start: 0.7877 (tt0) cc_final: 0.7521 (tt0) REVERT: H 158 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8389 (p) REVERT: L 24 ARG cc_start: 0.8262 (ttm170) cc_final: 0.7824 (ttm-80) REVERT: L 188 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7733 (ttmt) outliers start: 20 outliers final: 15 residues processed: 67 average time/residue: 0.0649 time to fit residues: 5.4426 Evaluate side-chains 71 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 46 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.0030 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.0020 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.125884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.090799 restraints weight = 5199.055| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.06 r_work: 0.2921 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4499 Z= 0.096 Angle : 0.519 6.517 6115 Z= 0.259 Chirality : 0.041 0.175 688 Planarity : 0.005 0.066 783 Dihedral : 4.235 29.117 621 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.46 % Allowed : 20.98 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: 1.38 (0.36), residues: 573 helix: 0.54 (1.09), residues: 23 sheet: 1.46 (0.33), residues: 252 loop : 0.57 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 142 TYR 0.010 0.001 TYR A 116 PHE 0.009 0.001 PHE A 149 TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 4494) covalent geometry : angle 0.51750 / 0.26 ( 6105) SS BOND : bond 0.00230 / 0.12 ( 5) SS BOND : angle 1.03788 / 0.54 ( 10) hydrogen bonds : bond 0.02610 / 1.68 ( 174) hydrogen bonds : angle 4.63723 / 3.18 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1139.77 seconds wall clock time: 20 minutes 8.85 seconds (1208.85 seconds total)