Starting phenix.real_space_refine on Tue Aug 4 14:12:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13bf_76938/08_2026/13bf_76938.cif Found real_map, /net/cci-nas-00/data/ceres_data/13bf_76938/08_2026/13bf_76938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13bf_76938/08_2026/13bf_76938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13bf_76938/08_2026/13bf_76938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13bf_76938/08_2026/13bf_76938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13bf_76938/08_2026/13bf_76938.map" } resolution = 3.0 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 19 5.16 5 C 2340 2.51 5 N 628 2.21 5 O 742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 3729 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1663 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 209} Chain: "L" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1655 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203} Chain: "A" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 411 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Time building chain proxies: 0.97, per 1000 atoms: 0.26 Number of scatterers: 3729 At special positions: 0 Unit cell: (60.976, 98.88, 77.456, 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 19 16.00 O 742 8.00 N 628 7.00 C 2340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 64 " 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: 0.28 Conformation dependent library (CDL) restraints added in 132.6 milliseconds 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 12 sheets defined 8.8% alpha, 47.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 191 through 196 removed outlier: 4.557A pdb=" N THR H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.064A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.844A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.973A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.755A pdb=" N CYS H 96 " --> pdb=" O TRP H 107 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TRP H 107 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG H 98 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP H 105 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.251A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.251A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.382A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.763A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.528A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.626A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AB3, first strand: chain 'A' and resid 34 through 37 178 hydrogen bonds defined for protein. 441 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: 0.35 Time building geometry restraints manager: 0.40 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: 1191 1.34 - 1.46: 967 1.46 - 1.58: 1636 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3816 Sorted by residual: bond pdb=" CB GLN A 61 " pdb=" CG GLN A 61 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" N GLU H 152 " pdb=" CA GLU H 152 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.41e-02 5.03e+03 1.34e+00 bond pdb=" CB CYS H 144 " pdb=" SG CYS H 144 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.04e+00 bond pdb=" CB GLU L 144 " pdb=" CG GLU L 144 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CB GLU L 196 " pdb=" CG GLU L 196 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 3811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 5108 2.89 - 5.79: 62 5.79 - 8.68: 8 8.68 - 11.58: 0 11.58 - 14.47: 1 Bond angle restraints: 5179 Sorted by residual: angle pdb=" CA LEU H 145 " pdb=" CB LEU H 145 " pdb=" CG LEU H 145 " ideal model delta sigma weight residual 116.30 130.77 -14.47 3.50e+00 8.16e-02 1.71e+01 angle pdb=" N SER L 30 " pdb=" CA SER L 30 " pdb=" CB SER L 30 " ideal model delta sigma weight residual 114.17 110.10 4.07 1.14e+00 7.69e-01 1.27e+01 angle pdb=" CA GLN A 61 " pdb=" CB GLN A 61 " pdb=" CG GLN A 61 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" N GLU H 152 " pdb=" CA GLU H 152 " pdb=" C GLU H 152 " ideal model delta sigma weight residual 109.81 116.90 -7.09 2.21e+00 2.05e-01 1.03e+01 angle pdb=" C SER L 30 " pdb=" N SER L 31 " pdb=" CA SER L 31 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 ... (remaining 5174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 1910 17.41 - 34.83: 260 34.83 - 52.24: 86 52.24 - 69.66: 22 69.66 - 87.07: 6 Dihedral angle restraints: 2284 sinusoidal: 882 harmonic: 1402 Sorted by residual: dihedral pdb=" CB CYS H 144 " pdb=" SG CYS H 144 " pdb=" SG CYS H 200 " pdb=" CB CYS H 200 " ideal model delta sinusoidal sigma weight residual -86.00 -169.98 83.98 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CA TYR L 141 " pdb=" C TYR L 141 " pdb=" N PRO L 142 " pdb=" CA PRO L 142 " ideal model delta harmonic sigma weight residual 180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA SER H 119 " pdb=" C SER H 119 " pdb=" N THR H 120 " pdb=" CA THR H 120 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 2281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 334 0.030 - 0.060: 144 0.060 - 0.091: 43 0.091 - 0.121: 37 0.121 - 0.151: 10 Chirality restraints: 568 Sorted by residual: chirality pdb=" CA GLU L 144 " pdb=" N GLU L 144 " pdb=" C GLU L 144 " pdb=" CB GLU L 144 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA PRO L 142 " pdb=" N PRO L 142 " pdb=" C PRO L 142 " pdb=" CB PRO L 142 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA VAL H 146 " pdb=" N VAL H 146 " pdb=" C VAL H 146 " pdb=" CB VAL H 146 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 565 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 150 " 0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO H 151 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 151 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 151 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 152 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO H 153 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 120 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO L 121 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO L 121 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 121 " 0.020 5.00e-02 4.00e+02 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 82 2.67 - 3.23: 3255 3.23 - 3.79: 5691 3.79 - 4.34: 8095 4.34 - 4.90: 13407 Nonbonded interactions: 30530 Sorted by model distance: nonbonded pdb=" OE1 GLN L 125 " pdb=" OG SER L 132 " model vdw 2.115 3.040 nonbonded pdb=" NE2 GLN H 6 " pdb=" OG1 THR H 111 " model vdw 2.217 3.120 nonbonded pdb=" O VAL H 125 " pdb=" NZ LYS H 213 " model vdw 2.230 3.120 nonbonded pdb=" ND1 HIS H 204 " pdb=" OG SER H 207 " model vdw 2.269 3.120 nonbonded pdb=" N ASP L 171 " pdb=" OD1 ASP L 171 " model vdw 2.318 3.120 ... (remaining 30525 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=0.56 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: 1.660 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 4.790 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 0.035 3823 Z= 0.183 Angle : 0.834 14.474 5193 Z= 0.443 Chirality : 0.046 0.151 568 Planarity : 0.005 0.064 664 Dihedral : 18.142 87.071 1371 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.20 % Favored : 94.39 % Rotamer: Outliers : 5.05 % Allowed : 31.25 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.47 (0.37), residues: 481 helix: -0.36 (0.98), residues: 24 sheet: 1.27 (0.33), residues: 215 loop : -0.51 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.014 0.002 TYR L 141 PHE 0.012 0.001 PHE L 95 TRP 0.008 0.002 TRP H 36 HIS 0.003 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 3816) covalent geometry : angle 0.83161 / 0.44 ( 5179) SS BOND : bond 0.00426 / 0.22 ( 7) SS BOND : angle 1.47450 / 0.91 ( 14) hydrogen bonds : bond 0.12243 / 8.32 ( 151) hydrogen bonds : angle 7.23303 / 5.14 ( 441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: H 214 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8132 (ttpp) outliers start: 21 outliers final: 19 residues processed: 71 average time/residue: 0.5470 time to fit residues: 40.0529 Evaluate side-chains 65 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 195 CYS Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 62 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.190937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.153719 restraints weight = 4057.578| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.78 r_work: 0.3472 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3823 Z= 0.152 Angle : 0.712 11.314 5193 Z= 0.357 Chirality : 0.045 0.147 568 Planarity : 0.005 0.061 664 Dihedral : 7.816 56.484 559 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.20 % Favored : 94.39 % Rotamer: Outliers : 6.25 % Allowed : 26.20 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.68 (0.37), residues: 481 helix: 0.35 (1.04), residues: 24 sheet: 1.41 (0.33), residues: 215 loop : -0.43 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 85 TYR 0.021 0.002 TYR A 36 PHE 0.011 0.001 PHE L 95 TRP 0.009 0.001 TRP H 107 HIS 0.003 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 3816) covalent geometry : angle 0.70991 / 0.36 ( 5179) SS BOND : bond 0.00383 / 0.20 ( 7) SS BOND : angle 1.22254 / 0.80 ( 14) hydrogen bonds : bond 0.03264 / 2.14 ( 151) hydrogen bonds : angle 5.73765 / 4.07 ( 441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: H 1 GLN cc_start: 0.5790 (OUTLIER) cc_final: 0.5023 (pp30) REVERT: H 43 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: H 132 SER cc_start: 0.6580 (p) cc_final: 0.6351 (m) REVERT: H 210 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6811 (mmtt) REVERT: H 214 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8232 (ttpp) REVERT: L 33 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8774 (tm) REVERT: L 42 GLN cc_start: 0.8506 (mt0) cc_final: 0.8291 (mt0) REVERT: L 79 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7801 (mm-30) REVERT: L 188 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7698 (mt-10) outliers start: 26 outliers final: 14 residues processed: 74 average time/residue: 0.4845 time to fit residues: 37.0620 Evaluate side-chains 66 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 62 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 0.0670 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.0060 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.4734 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.196199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.160287 restraints weight = 4013.619| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.75 r_work: 0.3534 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3823 Z= 0.114 Angle : 0.642 9.183 5193 Z= 0.321 Chirality : 0.043 0.137 568 Planarity : 0.005 0.055 664 Dihedral : 7.064 55.312 547 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.61 % Favored : 93.97 % Rotamer: Outliers : 5.29 % Allowed : 28.12 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.78 (0.38), residues: 481 helix: 1.09 (1.09), residues: 24 sheet: 1.46 (0.33), residues: 215 loop : -0.42 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 85 TYR 0.016 0.001 TYR A 36 PHE 0.009 0.001 PHE L 95 TRP 0.014 0.001 TRP A 47 HIS 0.002 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 3816) covalent geometry : angle 0.64006 / 0.32 ( 5179) SS BOND : bond 0.00327 / 0.17 ( 7) SS BOND : angle 1.05964 / 0.70 ( 14) hydrogen bonds : bond 0.02801 / 1.85 ( 151) hydrogen bonds : angle 5.33869 / 3.77 ( 441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: H 1 GLN cc_start: 0.5823 (OUTLIER) cc_final: 0.4981 (pp30) REVERT: H 43 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: H 210 LYS cc_start: 0.7228 (mmtt) cc_final: 0.6887 (mmtt) REVERT: H 214 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8234 (ttpp) REVERT: L 33 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8714 (tm) REVERT: L 42 GLN cc_start: 0.8451 (mt0) cc_final: 0.8213 (mt0) REVERT: A 32 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.4938 (mm) REVERT: A 66 LYS cc_start: 0.5330 (OUTLIER) cc_final: 0.4946 (tmtm) outliers start: 22 outliers final: 13 residues processed: 68 average time/residue: 0.5557 time to fit residues: 39.0125 Evaluate side-chains 61 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 66 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.6022 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.187904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.151721 restraints weight = 3998.819| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.98 r_work: 0.3437 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3823 Z= 0.213 Angle : 0.739 9.121 5193 Z= 0.370 Chirality : 0.046 0.172 568 Planarity : 0.005 0.058 664 Dihedral : 7.288 58.975 543 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.03 % Favored : 93.56 % Rotamer: Outliers : 7.93 % Allowed : 25.72 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.64 (0.38), residues: 481 helix: 0.70 (1.09), residues: 24 sheet: 1.37 (0.33), residues: 213 loop : -0.47 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.013 0.002 TYR H 95 PHE 0.015 0.002 PHE L 95 TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 ( 3816) covalent geometry : angle 0.73667 / 0.37 ( 5179) SS BOND : bond 0.00396 / 0.20 ( 7) SS BOND : angle 1.32968 / 0.87 ( 14) hydrogen bonds : bond 0.03476 / 2.26 ( 151) hydrogen bonds : angle 5.91142 / 4.21 ( 441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 46 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: H 134 SER cc_start: 0.0754 (OUTLIER) cc_final: 0.0525 (m) REVERT: H 175 GLN cc_start: 0.8330 (mt0) cc_final: 0.7985 (mt0) REVERT: L 33 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8828 (tm) REVERT: L 79 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: L 188 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: A 24 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.5121 (mp0) REVERT: A 32 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5536 (mm) REVERT: A 66 LYS cc_start: 0.5578 (OUTLIER) cc_final: 0.5365 (tmtm) outliers start: 33 outliers final: 15 residues processed: 73 average time/residue: 0.5091 time to fit residues: 38.3593 Evaluate side-chains 68 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 66 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.189829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.158489 restraints weight = 3968.284| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.65 r_work: 0.3485 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3823 Z= 0.162 Angle : 0.685 8.628 5193 Z= 0.344 Chirality : 0.045 0.170 568 Planarity : 0.005 0.056 664 Dihedral : 6.970 58.934 543 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.41 % Favored : 94.18 % Rotamer: Outliers : 8.17 % Allowed : 25.72 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.67 (0.38), residues: 481 helix: 1.16 (1.15), residues: 24 sheet: 1.33 (0.33), residues: 213 loop : -0.45 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 143 TYR 0.010 0.002 TYR H 198 PHE 0.011 0.001 PHE L 95 TRP 0.009 0.002 TRP H 47 HIS 0.002 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 3816) covalent geometry : angle 0.68295 / 0.34 ( 5179) SS BOND : bond 0.00328 / 0.17 ( 7) SS BOND : angle 1.20967 / 0.79 ( 14) hydrogen bonds : bond 0.03053 / 1.99 ( 151) hydrogen bonds : angle 5.61386 / 4.00 ( 441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 47 time to evaluate : 0.134 Fit side-chains REVERT: H 1 GLN cc_start: 0.5898 (OUTLIER) cc_final: 0.5301 (mp10) REVERT: H 43 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: H 70 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7999 (mtt) REVERT: H 210 LYS cc_start: 0.7290 (mmtt) cc_final: 0.7019 (mmtt) REVERT: L 33 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8839 (tm) REVERT: L 104 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8457 (ttpt) REVERT: L 188 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: A 32 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5453 (mm) REVERT: A 66 LYS cc_start: 0.5588 (OUTLIER) cc_final: 0.5230 (tmtm) outliers start: 34 outliers final: 18 residues processed: 75 average time/residue: 0.5051 time to fit residues: 39.2988 Evaluate side-chains 71 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 66 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.188291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.151897 restraints weight = 3971.346| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.86 r_work: 0.3451 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3823 Z= 0.197 Angle : 0.724 9.269 5193 Z= 0.363 Chirality : 0.046 0.155 568 Planarity : 0.005 0.058 664 Dihedral : 7.059 56.801 543 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.82 % Favored : 93.76 % Rotamer: Outliers : 7.69 % Allowed : 25.72 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.55 (0.38), residues: 481 helix: 0.89 (1.12), residues: 24 sheet: 1.29 (0.33), residues: 213 loop : -0.54 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.012 0.002 TYR H 95 PHE 0.014 0.001 PHE L 95 TRP 0.010 0.002 TRP H 47 HIS 0.002 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 3816) covalent geometry : angle 0.72174 / 0.36 ( 5179) SS BOND : bond 0.00349 / 0.18 ( 7) SS BOND : angle 1.28805 / 0.85 ( 14) hydrogen bonds : bond 0.03314 / 2.14 ( 151) hydrogen bonds : angle 5.83129 / 4.16 ( 441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 46 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: H 1 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5539 (mp10) REVERT: H 43 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: H 70 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7900 (mtt) REVERT: H 134 SER cc_start: 0.0778 (OUTLIER) cc_final: 0.0568 (m) REVERT: L 33 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8814 (tm) REVERT: L 79 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: L 104 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8528 (ttpt) REVERT: L 188 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: A 24 GLU cc_start: 0.5769 (OUTLIER) cc_final: 0.5002 (mp0) REVERT: A 32 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5646 (mm) REVERT: A 66 LYS cc_start: 0.5639 (OUTLIER) cc_final: 0.5426 (tmtm) outliers start: 32 outliers final: 20 residues processed: 73 average time/residue: 0.4505 time to fit residues: 34.0777 Evaluate side-chains 75 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 44 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 66 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.0070 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.189304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.152959 restraints weight = 4004.247| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.02 r_work: 0.3449 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3823 Z= 0.166 Angle : 0.690 8.947 5193 Z= 0.346 Chirality : 0.045 0.151 568 Planarity : 0.005 0.054 664 Dihedral : 6.849 55.990 543 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.41 % Favored : 94.18 % Rotamer: Outliers : 7.69 % Allowed : 26.92 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.56 (0.38), residues: 481 helix: 1.17 (1.15), residues: 24 sheet: 1.29 (0.33), residues: 213 loop : -0.56 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 84 TYR 0.011 0.002 TYR H 198 PHE 0.012 0.001 PHE L 95 TRP 0.010 0.002 TRP H 47 HIS 0.002 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 3816) covalent geometry : angle 0.68822 / 0.35 ( 5179) SS BOND : bond 0.00325 / 0.17 ( 7) SS BOND : angle 1.17184 / 0.78 ( 14) hydrogen bonds : bond 0.03047 / 1.98 ( 151) hydrogen bonds : angle 5.67052 / 4.04 ( 441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 45 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: H 1 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.5752 (mp10) REVERT: H 43 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7690 (mp10) REVERT: H 70 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7888 (mtt) REVERT: L 33 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8803 (tm) REVERT: L 79 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: L 104 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8471 (ttpt) REVERT: L 188 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: A 24 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.4966 (mp0) REVERT: A 32 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5597 (mm) REVERT: A 66 LYS cc_start: 0.5658 (OUTLIER) cc_final: 0.5406 (tmtm) outliers start: 32 outliers final: 19 residues processed: 71 average time/residue: 0.4608 time to fit residues: 33.9598 Evaluate side-chains 71 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 42 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 66 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.192287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.156520 restraints weight = 3973.541| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.99 r_work: 0.3469 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3823 Z= 0.141 Angle : 0.659 8.704 5193 Z= 0.331 Chirality : 0.044 0.140 568 Planarity : 0.005 0.053 664 Dihedral : 6.636 56.043 543 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.99 % Favored : 94.59 % Rotamer: Outliers : 7.21 % Allowed : 27.40 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.65 (0.38), residues: 481 helix: 1.44 (1.17), residues: 24 sheet: 1.34 (0.33), residues: 213 loop : -0.52 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 84 TYR 0.010 0.001 TYR H 198 PHE 0.010 0.001 PHE L 95 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 3816) covalent geometry : angle 0.65712 / 0.33 ( 5179) SS BOND : bond 0.00312 / 0.16 ( 7) SS BOND : angle 1.13016 / 0.75 ( 14) hydrogen bonds : bond 0.02839 / 1.85 ( 151) hydrogen bonds : angle 5.52207 / 3.91 ( 441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 43 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: H 1 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.5769 (mp10) REVERT: H 43 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: H 70 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7846 (mtt) REVERT: L 33 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8797 (tm) REVERT: L 50 ASP cc_start: 0.8197 (m-30) cc_final: 0.7977 (m-30) REVERT: L 79 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7511 (mm-30) REVERT: L 188 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: L 191 LYS cc_start: 0.6803 (mptt) cc_final: 0.5987 (tppt) REVERT: A 66 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5449 (tmtm) outliers start: 30 outliers final: 16 residues processed: 69 average time/residue: 0.5025 time to fit residues: 35.9359 Evaluate side-chains 64 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 66 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.0000 chunk 7 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.189764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.150472 restraints weight = 3957.274| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.80 r_work: 0.3459 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3823 Z= 0.162 Angle : 0.688 9.317 5193 Z= 0.344 Chirality : 0.045 0.149 568 Planarity : 0.005 0.054 664 Dihedral : 6.554 56.291 539 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.61 % Favored : 93.97 % Rotamer: Outliers : 6.97 % Allowed : 27.64 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.65 (0.38), residues: 481 helix: 1.32 (1.15), residues: 24 sheet: 1.33 (0.34), residues: 213 loop : -0.49 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 84 TYR 0.011 0.002 TYR H 95 PHE 0.012 0.001 PHE L 95 TRP 0.010 0.002 TRP A 47 HIS 0.002 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 3816) covalent geometry : angle 0.68579 / 0.34 ( 5179) SS BOND : bond 0.00325 / 0.17 ( 7) SS BOND : angle 1.19378 / 0.78 ( 14) hydrogen bonds : bond 0.03036 / 1.98 ( 151) hydrogen bonds : angle 5.63118 / 4.00 ( 441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: H 1 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.5815 (mp10) REVERT: H 43 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: H 70 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7794 (mtt) REVERT: H 210 LYS cc_start: 0.7169 (mmtt) cc_final: 0.6797 (tptt) REVERT: L 33 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8792 (tm) REVERT: L 79 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: L 188 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: A 32 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.4045 (pt) REVERT: A 62 LYS cc_start: 0.5004 (OUTLIER) cc_final: 0.4585 (pmmt) REVERT: A 66 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5543 (tmtm) outliers start: 29 outliers final: 19 residues processed: 66 average time/residue: 0.4762 time to fit residues: 32.5357 Evaluate side-chains 68 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 66 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.189360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.152725 restraints weight = 4034.066| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.95 r_work: 0.3458 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3823 Z= 0.168 Angle : 0.695 9.262 5193 Z= 0.348 Chirality : 0.045 0.153 568 Planarity : 0.005 0.055 664 Dihedral : 6.581 56.518 539 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.20 % Favored : 94.39 % Rotamer: Outliers : 6.97 % Allowed : 27.40 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.63 (0.38), residues: 481 helix: 1.30 (1.16), residues: 24 sheet: 1.31 (0.34), residues: 213 loop : -0.49 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 84 TYR 0.011 0.002 TYR H 95 PHE 0.013 0.001 PHE L 95 TRP 0.009 0.002 TRP H 107 HIS 0.002 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 3816) covalent geometry : angle 0.69353 / 0.35 ( 5179) SS BOND : bond 0.00326 / 0.17 ( 7) SS BOND : angle 1.20500 / 0.79 ( 14) hydrogen bonds : bond 0.03053 / 1.99 ( 151) hydrogen bonds : angle 5.67603 / 4.03 ( 441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: H 70 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7767 (mtt) REVERT: H 210 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6699 (mmmt) REVERT: L 33 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8788 (tm) REVERT: L 79 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7484 (mm-30) REVERT: L 188 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: A 32 LEU cc_start: 0.5594 (OUTLIER) cc_final: 0.4091 (pt) REVERT: A 62 LYS cc_start: 0.5153 (OUTLIER) cc_final: 0.4747 (pmmt) outliers start: 29 outliers final: 21 residues processed: 66 average time/residue: 0.5107 time to fit residues: 34.8845 Evaluate side-chains 68 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 62 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.193769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3718 r_free = 0.3718 target = 0.160037 restraints weight = 3944.281| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.75 r_work: 0.3553 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3823 Z= 0.120 Angle : 0.643 9.116 5193 Z= 0.321 Chirality : 0.044 0.138 568 Planarity : 0.004 0.052 664 Dihedral : 6.326 57.849 539 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.78 % Favored : 94.80 % Rotamer: Outliers : 6.01 % Allowed : 28.37 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.73 (0.38), residues: 481 helix: 1.60 (1.17), residues: 24 sheet: 1.33 (0.33), residues: 213 loop : -0.40 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 85 TYR 0.010 0.001 TYR L 141 PHE 0.009 0.001 PHE L 95 TRP 0.008 0.001 TRP H 107 HIS 0.002 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 3816) covalent geometry : angle 0.64171 / 0.32 ( 5179) SS BOND : bond 0.00293 / 0.15 ( 7) SS BOND : angle 1.06660 / 0.70 ( 14) hydrogen bonds : bond 0.02667 / 1.75 ( 151) hydrogen bonds : angle 5.33826 / 3.77 ( 441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1644.27 seconds wall clock time: 28 minutes 47.04 seconds (1727.04 seconds total)