Starting phenix.real_space_refine on Thu Oct 22 19:16:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29in_57198/10_2026/29in_57198.cif Found real_map, /net/cci-nas-00/data/ceres_data/29in_57198/10_2026/29in_57198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/29in_57198/10_2026/29in_57198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29in_57198/10_2026/29in_57198.map" model { file = "/net/cci-nas-00/data/ceres_data/29in_57198/10_2026/29in_57198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29in_57198/10_2026/29in_57198.cif" } resolution = 3.5 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= 0.011 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 14 5.16 5 C 2492 2.51 5 N 683 2.21 5 O 790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3979 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 608 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 82} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 5, 'GLU:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1710 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 212} Time building chain proxies: 0.79, per 1000 atoms: 0.20 Number of scatterers: 3979 At special positions: 0 Unit cell: (106.24, 65.57, 88.81, 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 14 16.00 O 790 8.00 N 683 7.00 C 2492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 214 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " 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: 0.16 Conformation dependent library (CDL) restraints added in 86.0 milliseconds 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 6.8% alpha, 47.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.737A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.875A pdb=" N VAL H 67 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.666A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.851A pdb=" N LEU A 155 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE A 138 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 153 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.749A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.588A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY L 95A" --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.588A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 144 through 150 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.502A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.016A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL H 96 " --> pdb=" O CYS H 100D" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.502A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.016A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.390A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.390A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 177 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 150 through 154 removed outlier: 4.738A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 462 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: 0.31 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1302 1.35 - 1.46: 984 1.46 - 1.58: 1766 1.58 - 1.70: 0 1.70 - 1.82: 15 Bond restraints: 4067 Sorted by residual: bond pdb=" CA CYS A 195 " pdb=" CB CYS A 195 " ideal model delta sigma weight residual 1.526 1.545 -0.019 1.53e-02 4.27e+03 1.49e+00 bond pdb=" CA HIS A 198 " pdb=" C HIS A 198 " ideal model delta sigma weight residual 1.520 1.533 -0.012 1.20e-02 6.94e+03 1.03e+00 bond pdb=" CA LEU L 13 " pdb=" CB LEU L 13 " ideal model delta sigma weight residual 1.535 1.522 0.012 1.32e-02 5.74e+03 8.82e-01 bond pdb=" C GLU L 79 " pdb=" N PRO L 80 " ideal model delta sigma weight residual 1.337 1.346 -0.009 9.80e-03 1.04e+04 8.57e-01 bond pdb=" C ARG A 159 " pdb=" O ARG A 159 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.59e-01 ... (remaining 4062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 5258 1.35 - 2.71: 221 2.71 - 4.06: 46 4.06 - 5.41: 21 5.41 - 6.76: 1 Bond angle restraints: 5547 Sorted by residual: angle pdb=" N THR L 72 " pdb=" CA THR L 72 " pdb=" C THR L 72 " ideal model delta sigma weight residual 107.88 112.78 -4.90 1.41e+00 5.03e-01 1.21e+01 angle pdb=" N SER L 22 " pdb=" CA SER L 22 " pdb=" C SER L 22 " ideal model delta sigma weight residual 107.49 112.45 -4.96 1.74e+00 3.30e-01 8.14e+00 angle pdb=" CA GLY L 66 " pdb=" C GLY L 66 " pdb=" O GLY L 66 " ideal model delta sigma weight residual 122.22 120.59 1.63 6.50e-01 2.37e+00 6.32e+00 angle pdb=" N GLY L 50 " pdb=" CA GLY L 50 " pdb=" C GLY L 50 " ideal model delta sigma weight residual 115.47 112.23 3.24 1.31e+00 5.83e-01 6.11e+00 angle pdb=" N GLY L 66 " pdb=" CA GLY L 66 " pdb=" C GLY L 66 " ideal model delta sigma weight residual 111.95 114.30 -2.35 9.50e-01 1.11e+00 6.10e+00 ... (remaining 5542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2251 17.98 - 35.96: 153 35.96 - 53.93: 31 53.93 - 71.91: 5 71.91 - 89.89: 5 Dihedral angle restraints: 2445 sinusoidal: 916 harmonic: 1529 Sorted by residual: dihedral pdb=" CB CYS L 214 " pdb=" SG CYS L 214 " pdb=" SG CYS H 216 " pdb=" CB CYS H 216 " ideal model delta sinusoidal sigma weight residual 93.00 159.28 -66.28 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 57.47 35.53 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CA ARG A 167 " pdb=" C ARG A 167 " pdb=" N GLN A 168 " pdb=" CA GLN A 168 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 350 0.028 - 0.057: 183 0.057 - 0.085: 46 0.085 - 0.113: 50 0.113 - 0.142: 8 Chirality restraints: 637 Sorted by residual: chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL H 184 " pdb=" N VAL H 184 " pdb=" C VAL H 184 " pdb=" CB VAL H 184 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 634 not shown) Planarity restraints: 717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO H 14 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO L 40 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 166 " 0.020 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO H 167 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 167 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 167 " 0.017 5.00e-02 4.00e+02 ... (remaining 714 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 575 2.77 - 3.30: 3530 3.30 - 3.83: 6093 3.83 - 4.37: 6814 4.37 - 4.90: 12564 Nonbonded interactions: 29576 Sorted by model distance: nonbonded pdb=" ND2 ASN H 197 " pdb=" OD1 ASP H 208 " model vdw 2.232 3.120 nonbonded pdb=" O TRP H 47 " pdb=" ND2 ASN H 60 " model vdw 2.250 3.120 nonbonded pdb=" NZ LYS H 206 " pdb=" OD1 ASP H 208 " model vdw 2.291 3.120 nonbonded pdb=" NH1 ARG L 54 " pdb=" OD1 ASP L 60 " model vdw 2.291 3.120 nonbonded pdb=" OG SER A 207 " pdb=" NH1 ARG A 209 " model vdw 2.292 3.120 ... (remaining 29571 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 group one per residue 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: 2.720 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: 0.000 Set scattering table: 0.010 Process input model: 3.310 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4073 Z= 0.141 Angle : 0.692 6.763 5559 Z= 0.376 Chirality : 0.043 0.142 637 Planarity : 0.004 0.042 717 Dihedral : 13.347 89.890 1449 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.37), residues: 526 helix: -0.31 (1.12), residues: 22 sheet: 0.34 (0.36), residues: 230 loop : -1.09 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 211 TYR 0.019 0.002 TYR H 176 PHE 0.014 0.002 PHE H 78 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 4067) covalent geometry : angle 0.69212 / 0.38 ( 5547) SS BOND : bond 0.00183 / 0.13 ( 6) SS BOND : angle 0.83867 / 0.46 ( 12) hydrogen bonds : bond 0.13311 / 9.58 ( 155) hydrogen bonds : angle 7.28298 / 5.09 ( 462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.154 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0278 time to fit residues: 1.7846 Evaluate side-chains 35 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [24, 48, 26, 2, 16, 32, 31, 25, 50, 19, 30] chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.178657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.147147 restraints weight = 5510.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150576 restraints weight = 3797.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152905 restraints weight = 2901.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.154598 restraints weight = 2395.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.155599 restraints weight = 2094.767| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 4073 Z= 0.166 Angle : 0.665 7.281 5559 Z= 0.334 Chirality : 0.045 0.153 637 Planarity : 0.005 0.037 717 Dihedral : 4.765 18.998 574 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.36 % Allowed : 8.16 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.59 (0.37), residues: 526 helix: -0.20 (1.15), residues: 22 sheet: 0.44 (0.36), residues: 227 loop : -1.14 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 211 TYR 0.016 0.002 TYR H 176 PHE 0.017 0.002 PHE L 139 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 4067) covalent geometry : angle 0.66407 / 0.33 ( 5547) SS BOND : bond 0.00355 / 0.26 ( 6) SS BOND : angle 0.91956 / 0.52 ( 12) hydrogen bonds : bond 0.03496 / 2.48 ( 155) hydrogen bonds : angle 5.93642 / 4.19 ( 462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.103 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 39 average time/residue: 0.0512 time to fit residues: 2.7490 Evaluate side-chains 38 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [18, 22, 32, 20, 30, 40, 48, 47, 29, 45, 16] chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146115 restraints weight = 5427.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149402 restraints weight = 3711.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.151492 restraints weight = 2850.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.153301 restraints weight = 2394.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.154357 restraints weight = 2079.055| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 4073 Z= 0.161 Angle : 0.637 5.547 5559 Z= 0.324 Chirality : 0.045 0.156 637 Planarity : 0.005 0.044 717 Dihedral : 4.800 19.321 574 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.04 % Allowed : 11.11 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.50 (0.37), residues: 526 helix: -0.09 (1.16), residues: 22 sheet: 0.58 (0.36), residues: 227 loop : -1.17 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 211 TYR 0.014 0.002 TYR H 35 PHE 0.017 0.002 PHE L 139 TRP 0.012 0.001 TRP H 103 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 ( 4067) covalent geometry : angle 0.63614 / 0.32 ( 5547) SS BOND : bond 0.00371 / 0.27 ( 6) SS BOND : angle 0.85429 / 0.47 ( 12) hydrogen bonds : bond 0.03282 / 2.30 ( 155) hydrogen bonds : angle 5.60499 / 3.96 ( 462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.145 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 36 average time/residue: 0.0530 time to fit residues: 2.6765 Evaluate side-chains 36 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain H residue 53 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [21, 38, 50, 29, 1, 34, 43, 46, 31, 25, 18] chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.0040 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.175792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144088 restraints weight = 5447.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147567 restraints weight = 3674.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.150041 restraints weight = 2793.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.151455 restraints weight = 2297.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.152722 restraints weight = 2019.641| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 4073 Z= 0.186 Angle : 0.663 5.477 5559 Z= 0.338 Chirality : 0.046 0.161 637 Planarity : 0.005 0.049 717 Dihedral : 4.902 19.540 574 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.17 % Allowed : 12.70 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.53 (0.37), residues: 526 helix: 0.10 (1.16), residues: 21 sheet: 0.61 (0.36), residues: 227 loop : -1.26 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 211 TYR 0.016 0.002 TYR L 49 PHE 0.021 0.003 PHE L 139 TRP 0.015 0.002 TRP H 47 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 ( 4067) covalent geometry : angle 0.66298 / 0.34 ( 5547) SS BOND : bond 0.00428 / 0.30 ( 6) SS BOND : angle 0.85240 / 0.47 ( 12) hydrogen bonds : bond 0.03417 / 2.39 ( 155) hydrogen bonds : angle 5.63170 / 3.99 ( 462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.148 Fit side-chains REVERT: L 116 PHE cc_start: 0.5730 (m-10) cc_final: 0.5358 (m-10) outliers start: 14 outliers final: 9 residues processed: 42 average time/residue: 0.0501 time to fit residues: 2.9126 Evaluate side-chains 40 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain H residue 53 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [46, 25, 11, 19, 32, 37, 3, 33, 9, 30, 12] chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 32 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.0070 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.185260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.152230 restraints weight = 5549.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155784 restraints weight = 3782.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158158 restraints weight = 2884.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160047 restraints weight = 2382.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.161075 restraints weight = 2076.399| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4073 Z= 0.108 Angle : 0.574 5.223 5559 Z= 0.290 Chirality : 0.043 0.138 637 Planarity : 0.004 0.045 717 Dihedral : 4.520 19.534 574 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.04 % Allowed : 14.51 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.31 (0.38), residues: 526 helix: 0.33 (1.21), residues: 21 sheet: 0.56 (0.36), residues: 239 loop : -0.97 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 211 TYR 0.015 0.002 TYR H 176 PHE 0.012 0.001 PHE H 78 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 4067) covalent geometry : angle 0.57419 / 0.29 ( 5547) SS BOND : bond 0.00162 / 0.12 ( 6) SS BOND : angle 0.52951 / 0.31 ( 12) hydrogen bonds : bond 0.02538 / 1.78 ( 155) hydrogen bonds : angle 5.24129 / 3.72 ( 462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.158 Fit side-chains REVERT: L 116 PHE cc_start: 0.5843 (m-10) cc_final: 0.5412 (m-10) outliers start: 9 outliers final: 7 residues processed: 37 average time/residue: 0.0708 time to fit residues: 3.4575 Evaluate side-chains 37 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [36, 30, 2, 21, 45, 37, 31, 22, 16, 39, 42] chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.178470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145374 restraints weight = 5684.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148728 restraints weight = 3897.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151082 restraints weight = 3003.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.152523 restraints weight = 2510.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.153681 restraints weight = 2219.797| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 4073 Z= 0.252 Angle : 0.734 6.078 5559 Z= 0.375 Chirality : 0.047 0.171 637 Planarity : 0.005 0.055 717 Dihedral : 5.188 20.711 574 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.95 % Allowed : 15.65 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.37), residues: 526 helix: -0.15 (1.09), residues: 21 sheet: 0.63 (0.36), residues: 233 loop : -1.44 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 211 TYR 0.021 0.003 TYR H 176 PHE 0.031 0.003 PHE L 139 TRP 0.017 0.002 TRP H 47 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.25 ( 4067) covalent geometry : angle 0.73337 / 0.37 ( 5547) SS BOND : bond 0.00555 / 0.37 ( 6) SS BOND : angle 1.03268 / 0.56 ( 12) hydrogen bonds : bond 0.03955 / 2.76 ( 155) hydrogen bonds : angle 5.80428 / 4.13 ( 462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.148 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 47 average time/residue: 0.0501 time to fit residues: 3.3027 Evaluate side-chains 44 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain H residue 53 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [28, 0, 33, 38, 6, 10, 41, 13, 19, 42, 20] chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.182434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149651 restraints weight = 5627.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153118 restraints weight = 3782.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.155531 restraints weight = 2900.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156933 restraints weight = 2407.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158417 restraints weight = 2126.952| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 4073 Z= 0.129 Angle : 0.604 5.212 5559 Z= 0.308 Chirality : 0.044 0.146 637 Planarity : 0.005 0.048 717 Dihedral : 4.801 20.522 574 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.40 % Allowed : 16.33 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 526 helix: 0.23 (1.19), residues: 21 sheet: 0.60 (0.36), residues: 234 loop : -1.21 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 211 TYR 0.013 0.002 TYR L 49 PHE 0.014 0.002 PHE L 116 TRP 0.015 0.001 TRP H 47 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 4067) covalent geometry : angle 0.60369 / 0.31 ( 5547) SS BOND : bond 0.00238 / 0.18 ( 6) SS BOND : angle 0.62093 / 0.35 ( 12) hydrogen bonds : bond 0.02750 / 1.92 ( 155) hydrogen bonds : angle 5.39878 / 3.84 ( 462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.102 Fit side-chains REVERT: L 116 PHE cc_start: 0.5540 (m-10) cc_final: 0.5302 (m-10) outliers start: 15 outliers final: 12 residues processed: 44 average time/residue: 0.0505 time to fit residues: 3.0912 Evaluate side-chains 43 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [47, 37, 18, 12, 1, 9, 45, 40, 19, 7, 11] chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.181938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.148670 restraints weight = 5589.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152146 restraints weight = 3800.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.154567 restraints weight = 2921.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.156230 restraints weight = 2434.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.157201 restraints weight = 2138.044| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 4073 Z= 0.152 Angle : 0.618 5.214 5559 Z= 0.315 Chirality : 0.044 0.151 637 Planarity : 0.005 0.050 717 Dihedral : 4.743 19.574 574 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.17 % Allowed : 17.69 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.45 (0.37), residues: 526 helix: 0.18 (1.15), residues: 21 sheet: 0.55 (0.36), residues: 235 loop : -1.13 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 211 TYR 0.014 0.002 TYR L 49 PHE 0.017 0.002 PHE L 139 TRP 0.018 0.002 TRP H 47 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.15 ( 4067) covalent geometry : angle 0.61816 / 0.31 ( 5547) SS BOND : bond 0.00316 / 0.23 ( 6) SS BOND : angle 0.73904 / 0.40 ( 12) hydrogen bonds : bond 0.02972 / 2.07 ( 155) hydrogen bonds : angle 5.39039 / 3.83 ( 462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.159 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 44 average time/residue: 0.0470 time to fit residues: 2.9625 Evaluate side-chains 46 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [34, 29, 12, 22, 17, 43, 36, 16, 50, 7, 39] chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.182535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.149124 restraints weight = 5651.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.152689 restraints weight = 3824.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154817 restraints weight = 2928.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.156688 restraints weight = 2466.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.157710 restraints weight = 2155.195| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 4073 Z= 0.148 Angle : 0.613 5.226 5559 Z= 0.313 Chirality : 0.044 0.149 637 Planarity : 0.005 0.050 717 Dihedral : 4.725 19.663 574 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.63 % Allowed : 17.01 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.43 (0.37), residues: 526 helix: 0.25 (1.17), residues: 21 sheet: 0.55 (0.36), residues: 235 loop : -1.11 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 211 TYR 0.018 0.002 TYR H 176 PHE 0.016 0.002 PHE L 139 TRP 0.018 0.002 TRP H 47 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 4067) covalent geometry : angle 0.61282 / 0.31 ( 5547) SS BOND : bond 0.00297 / 0.22 ( 6) SS BOND : angle 0.69803 / 0.38 ( 12) hydrogen bonds : bond 0.02893 / 2.02 ( 155) hydrogen bonds : angle 5.34903 / 3.81 ( 462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.149 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 45 average time/residue: 0.0444 time to fit residues: 2.8181 Evaluate side-chains 46 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [47, 12, 34, 21, 23, 7, 36, 33, 46, 22, 13] chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.183176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.150319 restraints weight = 5560.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153904 restraints weight = 3717.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.156408 restraints weight = 2820.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.157817 restraints weight = 2339.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.159153 restraints weight = 2064.438| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4073 Z= 0.122 Angle : 0.586 5.001 5559 Z= 0.298 Chirality : 0.043 0.142 637 Planarity : 0.005 0.048 717 Dihedral : 4.547 19.485 574 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.17 % Allowed : 17.46 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.32 (0.38), residues: 526 helix: 0.35 (1.19), residues: 21 sheet: 0.59 (0.36), residues: 235 loop : -0.99 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 211 TYR 0.017 0.002 TYR H 176 PHE 0.013 0.002 PHE L 139 TRP 0.018 0.002 TRP H 47 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.12 ( 4067) covalent geometry : angle 0.58581 / 0.30 ( 5547) SS BOND : bond 0.00214 / 0.16 ( 6) SS BOND : angle 0.61579 / 0.34 ( 12) hydrogen bonds : bond 0.02611 / 1.82 ( 155) hydrogen bonds : angle 5.20715 / 3.70 ( 462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.091 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 40 average time/residue: 0.0409 time to fit residues: 2.4152 Evaluate side-chains 43 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: [10, 25, 37, 45, 34, 24, 8, 12, 6, 42, 44] chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.182010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148859 restraints weight = 5622.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.152316 restraints weight = 3807.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.154808 restraints weight = 2922.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156230 restraints weight = 2429.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.157567 restraints weight = 2145.866| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 4073 Z= 0.151 Angle : 0.614 5.231 5559 Z= 0.312 Chirality : 0.044 0.150 637 Planarity : 0.005 0.050 717 Dihedral : 4.645 19.305 574 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.40 % Allowed : 17.23 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.34 (0.38), residues: 526 helix: 0.28 (1.17), residues: 21 sheet: 0.59 (0.36), residues: 235 loop : -1.01 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 211 TYR 0.019 0.002 TYR H 176 PHE 0.016 0.002 PHE L 139 TRP 0.018 0.002 TRP H 47 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 ( 4067) covalent geometry : angle 0.61331 / 0.31 ( 5547) SS BOND : bond 0.00303 / 0.22 ( 6) SS BOND : angle 0.72915 / 0.40 ( 12) hydrogen bonds : bond 0.02908 / 2.03 ( 155) hydrogen bonds : angle 5.29334 / 3.76 ( 462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 934.21 seconds wall clock time: 16 minutes 45.69 seconds (1005.69 seconds total)