Starting phenix.real_space_refine on Wed Sep 17 08:33:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hb3_52012/09_2025/9hb3_52012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hb3_52012/09_2025/9hb3_52012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hb3_52012/09_2025/9hb3_52012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hb3_52012/09_2025/9hb3_52012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hb3_52012/09_2025/9hb3_52012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hb3_52012/09_2025/9hb3_52012.map" } resolution = 2.5 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= 0.007 sd= 0.021 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 30 5.16 5 C 4546 2.51 5 N 1210 2.21 5 O 1353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7139 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 327 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "K" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 10, 'TRANS': 201} Chain: "R" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2566 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 11, 'TRANS': 335} Chain breaks: 8 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 11, 'HIS:plan': 2, 'PHE:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 103 Time building chain proxies: 2.10, per 1000 atoms: 0.29 Number of scatterers: 7139 At special positions: 0 Unit cell: (67.0032, 103.55, 156.341, 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 30 16.00 O 1353 8.00 N 1210 7.00 C 4546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 192 " 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: 0.63 Conformation dependent library (CDL) restraints added in 410.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.7% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.779A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 200 through 205 Processing helix chain 'H' and resid 216 through 218 No H-bonds generated for 'chain 'H' and resid 216 through 218' Processing helix chain 'K' and resid 74 through 76 No H-bonds generated for 'chain 'K' and resid 74 through 76' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.598A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.012A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 129 Processing helix chain 'L' and resid 185 through 191 removed outlier: 3.901A pdb=" N HIS L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 66 Processing helix chain 'R' and resid 67 through 69 No H-bonds generated for 'chain 'R' and resid 67 through 69' Processing helix chain 'R' and resid 72 through 101 removed outlier: 3.719A pdb=" N VAL R 76 " --> pdb=" O ALA R 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE R 77 " --> pdb=" O PRO R 73 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 110 through 141 removed outlier: 3.992A pdb=" N LYS R 116 " --> pdb=" O CYS R 112 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER R 127 " --> pdb=" O MET R 123 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE R 130 " --> pdb=" O SER R 126 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE R 141 " --> pdb=" O ARG R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 170 Processing helix chain 'R' and resid 173 through 178 removed outlier: 3.655A pdb=" N PHE R 178 " --> pdb=" O GLN R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 214 Processing helix chain 'R' and resid 214 through 234 Processing helix chain 'R' and resid 265 through 297 Proline residue: R 286 - end of helix Processing helix chain 'R' and resid 307 through 316 Processing helix chain 'R' and resid 316 through 329 Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 329 through 336 Processing helix chain 'R' and resid 501 through 524 Processing helix chain 'R' and resid 526 through 547 Processing helix chain 'R' and resid 563 through 585 Processing helix chain 'R' and resid 587 through 611 removed outlier: 3.753A pdb=" N LEU R 598 " --> pdb=" O ALA R 594 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS R 599 " --> pdb=" O ALA R 595 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR R 600 " --> pdb=" O GLU R 596 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS R 608 " --> pdb=" O ALA R 604 " (cutoff:3.500A) Processing helix chain 'R' and resid 612 through 615 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 22 Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.153A pdb=" N GLY H 13 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 136 removed outlier: 5.924A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 136 removed outlier: 5.924A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 149 through 151 Processing sheet with id=AA7, first strand: chain 'H' and resid 164 through 168 Processing sheet with id=AA8, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 12 removed outlier: 4.073A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.335A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.335A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.164A pdb=" N SER L 133 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU L 183 " --> pdb=" O SER L 133 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL L 135 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU L 181 " --> pdb=" O VAL L 135 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU L 137 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER L 179 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN L 139 " --> pdb=" O LEU L 177 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU L 177 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 155 through 156 410 hydrogen bonds defined for protein. 1110 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: 1.29 Time building geometry restraints manager: 0.87 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: 2255 1.34 - 1.46: 1555 1.46 - 1.58: 3448 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 7299 Sorted by residual: bond pdb=" N ASN A 6 " pdb=" CA ASN A 6 " ideal model delta sigma weight residual 1.457 1.426 0.031 1.16e-02 7.43e+03 7.17e+00 bond pdb=" N GLN R 119 " pdb=" CA GLN R 119 " ideal model delta sigma weight residual 1.459 1.434 0.025 1.19e-02 7.06e+03 4.54e+00 bond pdb=" CA CYS A 5 " pdb=" C CYS A 5 " ideal model delta sigma weight residual 1.522 1.493 0.029 1.43e-02 4.89e+03 3.97e+00 bond pdb=" N LYS A 10 " pdb=" CA LYS A 10 " ideal model delta sigma weight residual 1.457 1.429 0.028 1.41e-02 5.03e+03 3.88e+00 bond pdb=" C ASN A 6 " pdb=" N LEU A 7 " ideal model delta sigma weight residual 1.333 1.364 -0.031 1.61e-02 3.86e+03 3.67e+00 ... (remaining 7294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 9747 1.88 - 3.77: 154 3.77 - 5.65: 29 5.65 - 7.53: 5 7.53 - 9.42: 1 Bond angle restraints: 9936 Sorted by residual: angle pdb=" N LYS A 10 " pdb=" CA LYS A 10 " pdb=" C LYS A 10 " ideal model delta sigma weight residual 109.81 100.39 9.42 2.21e+00 2.05e-01 1.82e+01 angle pdb=" C GLY K 16 " pdb=" N SER K 17 " pdb=" CA SER K 17 " ideal model delta sigma weight residual 121.63 115.63 6.00 1.92e+00 2.71e-01 9.78e+00 angle pdb=" N CYS A 5 " pdb=" CA CYS A 5 " pdb=" C CYS A 5 " ideal model delta sigma weight residual 112.87 109.18 3.69 1.20e+00 6.94e-01 9.44e+00 angle pdb=" N GLU H 162 " pdb=" CA GLU H 162 " pdb=" C GLU H 162 " ideal model delta sigma weight residual 109.81 115.66 -5.85 2.21e+00 2.05e-01 7.00e+00 angle pdb=" C THR R 615 " pdb=" N LEU R 616 " pdb=" CA LEU R 616 " ideal model delta sigma weight residual 121.70 126.31 -4.61 1.80e+00 3.09e-01 6.57e+00 ... (remaining 9931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 4088 17.06 - 34.11: 171 34.11 - 51.17: 33 51.17 - 68.22: 9 68.22 - 85.28: 5 Dihedral angle restraints: 4306 sinusoidal: 1549 harmonic: 2757 Sorted by residual: dihedral pdb=" CB CYS R 112 " pdb=" SG CYS R 112 " pdb=" SG CYS R 192 " pdb=" CB CYS R 192 " ideal model delta sinusoidal sigma weight residual 93.00 150.53 -57.53 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CA GLY K 15 " pdb=" C GLY K 15 " pdb=" N GLY K 16 " pdb=" CA GLY K 16 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA SER K 17 " pdb=" C SER K 17 " pdb=" N LEU K 18 " pdb=" CA LEU K 18 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 4303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 644 0.029 - 0.058: 331 0.058 - 0.088: 107 0.088 - 0.117: 42 0.117 - 0.146: 9 Chirality restraints: 1133 Sorted by residual: chirality pdb=" CA LYS A 10 " pdb=" N LYS A 10 " pdb=" C LYS A 10 " pdb=" CB LYS A 10 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE L 22 " pdb=" N ILE L 22 " pdb=" C ILE L 22 " pdb=" CB ILE L 22 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA VAL H 156 " pdb=" N VAL H 156 " pdb=" C VAL H 156 " pdb=" CB VAL H 156 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1130 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 10 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C LYS A 10 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS A 10 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO A 11 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 162 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO H 163 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO H 163 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 163 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 12 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO A 13 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 13 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 13 " 0.020 5.00e-02 4.00e+02 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 4128 3.02 - 3.49: 7234 3.49 - 3.96: 12178 3.96 - 4.43: 14102 4.43 - 4.90: 22176 Nonbonded interactions: 59818 Sorted by model distance: nonbonded pdb=" O LYS A 10 " pdb=" O PRO A 11 " model vdw 2.545 3.040 nonbonded pdb=" N CYS A 5 " pdb=" N ASN A 6 " model vdw 2.551 2.560 nonbonded pdb=" O ALA R 101 " pdb=" OG1 THR R 102 " model vdw 2.576 3.040 nonbonded pdb=" N GLU H 9 " pdb=" OE1 GLU H 9 " model vdw 2.612 3.120 nonbonded pdb=" N CYS R 142 " pdb=" O CYS R 142 " model vdw 2.615 2.496 ... (remaining 59813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4830 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 0.072 7306 Z= 0.209 Angle : 0.646 9.418 9950 Z= 0.356 Chirality : 0.041 0.146 1133 Planarity : 0.005 0.047 1258 Dihedral : 10.955 85.277 2505 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.95 % Allowed : 3.66 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 aren not related in a simple way. whole: 0.93 (0.28), residues: 923 helix: 1.04 (0.27), residues: 320 sheet: 0.88 (0.31), residues: 261 loop : 0.16 (0.38), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 104 TYR 0.015 0.002 TYR L 92 PHE 0.017 0.002 PHE R 287 TRP 0.014 0.002 TRP H 117 HIS 0.003 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 7299) covalent geometry : angle 0.64523 ( 9936) SS BOND : bond 0.00199 ( 7) SS BOND : angle 0.92858 ( 14) hydrogen bonds : bond 0.08466 ( 401) hydrogen bonds : angle 6.19355 ( 1110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.267 Fit side-chains REVERT: H 90 ARG cc_start: 0.3421 (mtt180) cc_final: 0.3088 (mtp-110) REVERT: H 126 SER cc_start: 0.6792 (t) cc_final: 0.6475 (p) REVERT: H 198 VAL cc_start: 0.5944 (m) cc_final: 0.5730 (m) REVERT: H 218 ASN cc_start: 0.6737 (m-40) cc_final: 0.6261 (t0) REVERT: K 12 VAL cc_start: 0.6783 (m) cc_final: 0.6426 (p) REVERT: K 29 ILE cc_start: 0.6560 (pt) cc_final: 0.6310 (pt) REVERT: K 70 VAL cc_start: 0.5785 (t) cc_final: 0.5548 (p) REVERT: K 82 GLN cc_start: 0.5618 (tp40) cc_final: 0.5201 (tp40) REVERT: L 43 LYS cc_start: 0.5897 (mttt) cc_final: 0.4891 (pttp) REVERT: L 124 ASP cc_start: 0.6807 (m-30) cc_final: 0.6460 (p0) REVERT: L 134 VAL cc_start: 0.6145 (t) cc_final: 0.5919 (m) REVERT: R 120 MET cc_start: 0.3385 (mmm) cc_final: 0.3042 (tpp) REVERT: R 225 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6466 (tm-30) REVERT: R 330 SER cc_start: 0.4855 (p) cc_final: 0.4518 (m) REVERT: R 564 ASP cc_start: 0.3774 (m-30) cc_final: 0.3291 (t0) outliers start: 7 outliers final: 2 residues processed: 152 average time/residue: 0.5799 time to fit residues: 93.0471 Evaluate side-chains 100 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 160 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN H 80 ASN H 213 ASN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS R 510 ASN R 607 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.184499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.161241 restraints weight = 12019.210| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 1.80 r_work: 0.4490 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4371 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7306 Z= 0.193 Angle : 0.644 8.238 9950 Z= 0.341 Chirality : 0.042 0.147 1133 Planarity : 0.005 0.063 1258 Dihedral : 5.389 46.576 1017 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.79 % Allowed : 9.89 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: 0.69 (0.28), residues: 923 helix: 0.98 (0.28), residues: 324 sheet: 0.49 (0.29), residues: 288 loop : 0.06 (0.39), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 101 TYR 0.018 0.002 TYR K 95 PHE 0.015 0.002 PHE K 59 TRP 0.019 0.002 TRP H 117 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7299) covalent geometry : angle 0.64235 ( 9936) SS BOND : bond 0.00534 ( 7) SS BOND : angle 1.31401 ( 14) hydrogen bonds : bond 0.04207 ( 401) hydrogen bonds : angle 5.21411 ( 1110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.275 Fit side-chains REVERT: H 53 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.6365 (p90) REVERT: H 219 THR cc_start: 0.7395 (m) cc_final: 0.7176 (m) REVERT: H 220 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7365 (mtmm) REVERT: L 43 LYS cc_start: 0.6900 (mttt) cc_final: 0.5738 (pttp) REVERT: L 141 PHE cc_start: 0.4751 (t80) cc_final: 0.3994 (t80) REVERT: L 157 GLN cc_start: 0.5230 (mm-40) cc_final: 0.4045 (mm110) REVERT: R 123 MET cc_start: 0.4468 (mtt) cc_final: 0.4003 (mpt) REVERT: R 564 ASP cc_start: 0.5031 (m-30) cc_final: 0.4477 (t70) outliers start: 28 outliers final: 14 residues processed: 128 average time/residue: 0.4794 time to fit residues: 65.5125 Evaluate side-chains 107 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 200 HIS Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 208 TRP Chi-restraints excluded: chain R residue 532 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 88 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN H 213 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.184208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.162031 restraints weight = 12089.002| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 1.72 r_work: 0.4529 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4411 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7306 Z= 0.130 Angle : 0.556 8.268 9950 Z= 0.291 Chirality : 0.040 0.133 1133 Planarity : 0.004 0.041 1258 Dihedral : 4.927 48.772 1016 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.25 % Allowed : 13.55 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 aren not related in a simple way. whole: 0.94 (0.28), residues: 923 helix: 1.25 (0.28), residues: 325 sheet: 0.61 (0.29), residues: 285 loop : 0.15 (0.39), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 31 TYR 0.024 0.002 TYR L 92 PHE 0.011 0.001 PHE H 160 TRP 0.012 0.002 TRP H 117 HIS 0.003 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7299) covalent geometry : angle 0.55559 ( 9936) SS BOND : bond 0.00237 ( 7) SS BOND : angle 0.95067 ( 14) hydrogen bonds : bond 0.03528 ( 401) hydrogen bonds : angle 4.80175 ( 1110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.298 Fit side-chains REVERT: H 53 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6043 (p90) REVERT: H 219 THR cc_start: 0.7357 (m) cc_final: 0.7064 (m) REVERT: H 220 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7523 (mppt) REVERT: L 43 LYS cc_start: 0.6899 (mttt) cc_final: 0.5784 (pttp) REVERT: L 141 PHE cc_start: 0.4614 (t80) cc_final: 0.3878 (t80) REVERT: L 157 GLN cc_start: 0.5251 (mm-40) cc_final: 0.4292 (mm-40) REVERT: R 564 ASP cc_start: 0.4972 (m-30) cc_final: 0.4476 (t70) outliers start: 24 outliers final: 13 residues processed: 120 average time/residue: 0.4943 time to fit residues: 63.3564 Evaluate side-chains 103 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 504 LEU Chi-restraints excluded: chain R residue 532 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN L 139 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 567 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.177282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.153919 restraints weight = 11883.142| |-----------------------------------------------------------------------------| r_work (start): 0.4497 rms_B_bonded: 1.77 r_work: 0.4412 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4295 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 7306 Z= 0.296 Angle : 0.759 9.456 9950 Z= 0.406 Chirality : 0.046 0.168 1133 Planarity : 0.006 0.069 1258 Dihedral : 5.945 44.367 1016 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.07 % Allowed : 15.31 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -0.02 (0.27), residues: 923 helix: 0.51 (0.28), residues: 320 sheet: 0.10 (0.31), residues: 276 loop : -0.44 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 41 TYR 0.030 0.003 TYR L 92 PHE 0.016 0.003 PHE K 59 TRP 0.031 0.003 TRP H 117 HIS 0.004 0.002 HIS R 567 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 7299) covalent geometry : angle 0.75674 ( 9936) SS BOND : bond 0.00417 ( 7) SS BOND : angle 1.64605 ( 14) hydrogen bonds : bond 0.04983 ( 401) hydrogen bonds : angle 5.78582 ( 1110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.309 Fit side-chains REVERT: L 43 LYS cc_start: 0.7382 (mttt) cc_final: 0.6066 (pttp) REVERT: L 141 PHE cc_start: 0.4558 (t80) cc_final: 0.3876 (t80) REVERT: L 142 TYR cc_start: 0.4901 (OUTLIER) cc_final: 0.4079 (m-80) REVERT: R 123 MET cc_start: 0.4174 (mtt) cc_final: 0.3652 (mmt) REVERT: R 562 MET cc_start: -0.0784 (OUTLIER) cc_final: -0.2523 (mtt) outliers start: 30 outliers final: 18 residues processed: 126 average time/residue: 0.4812 time to fit residues: 64.7816 Evaluate side-chains 114 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 128 LYS Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 208 TRP Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 532 ASP Chi-restraints excluded: chain R residue 562 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.0670 chunk 27 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN H 80 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.181651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.159247 restraints weight = 12089.030| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 1.76 r_work: 0.4482 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4365 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7306 Z= 0.128 Angle : 0.554 6.905 9950 Z= 0.294 Chirality : 0.040 0.131 1133 Planarity : 0.004 0.042 1258 Dihedral : 5.103 50.285 1016 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.47 % Allowed : 16.12 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 aren not related in a simple way. whole: 0.53 (0.28), residues: 923 helix: 1.08 (0.29), residues: 325 sheet: 0.35 (0.31), residues: 279 loop : -0.24 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.021 0.002 TYR L 92 PHE 0.027 0.002 PHE H 136 TRP 0.013 0.002 TRP H 117 HIS 0.005 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7299) covalent geometry : angle 0.55375 ( 9936) SS BOND : bond 0.00091 ( 7) SS BOND : angle 0.81634 ( 14) hydrogen bonds : bond 0.03527 ( 401) hydrogen bonds : angle 4.95713 ( 1110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 22 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6063 (ttp-170) REVERT: H 53 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.5983 (p90) REVERT: H 220 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7625 (mppt) REVERT: K 17 SER cc_start: 0.5913 (m) cc_final: 0.5653 (p) REVERT: L 43 LYS cc_start: 0.7186 (mttt) cc_final: 0.5994 (pttp) REVERT: L 211 PHE cc_start: 0.5536 (p90) cc_final: 0.4520 (p90) REVERT: R 44 LEU cc_start: 0.5905 (mm) cc_final: 0.5647 (mt) REVERT: R 123 MET cc_start: 0.4442 (mtt) cc_final: 0.3925 (mmt) REVERT: R 211 LEU cc_start: 0.6953 (tp) cc_final: 0.6752 (mt) REVERT: R 537 MET cc_start: 0.7425 (ttm) cc_final: 0.6891 (mtt) REVERT: R 564 ASP cc_start: 0.4662 (m-30) cc_final: 0.4392 (t70) outliers start: 33 outliers final: 18 residues processed: 129 average time/residue: 0.4673 time to fit residues: 64.4815 Evaluate side-chains 120 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain R residue 532 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.0050 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN L 139 ASN L 157 GLN L 160 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.179478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.158954 restraints weight = 11881.707| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 2.12 r_work: 0.4445 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4332 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7306 Z= 0.189 Angle : 0.640 8.182 9950 Z= 0.338 Chirality : 0.041 0.145 1133 Planarity : 0.005 0.045 1258 Dihedral : 5.360 48.793 1016 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.20 % Allowed : 17.62 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 aren not related in a simple way. whole: 0.39 (0.28), residues: 923 helix: 0.99 (0.29), residues: 325 sheet: 0.30 (0.31), residues: 276 loop : -0.39 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 101 TYR 0.026 0.002 TYR L 92 PHE 0.044 0.002 PHE H 136 TRP 0.020 0.002 TRP H 117 HIS 0.007 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 7299) covalent geometry : angle 0.63861 ( 9936) SS BOND : bond 0.00249 ( 7) SS BOND : angle 1.17041 ( 14) hydrogen bonds : bond 0.04060 ( 401) hydrogen bonds : angle 5.20985 ( 1110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.293 Fit side-chains REVERT: H 22 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6017 (ttp-170) REVERT: H 53 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6375 (p90) REVERT: H 155 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6936 (mt) REVERT: H 220 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7612 (mtmm) REVERT: K 17 SER cc_start: 0.6450 (m) cc_final: 0.6008 (p) REVERT: L 43 LYS cc_start: 0.7309 (mttt) cc_final: 0.6068 (pttp) REVERT: L 141 PHE cc_start: 0.4337 (t80) cc_final: 0.3595 (t80) REVERT: L 142 TYR cc_start: 0.4977 (OUTLIER) cc_final: 0.3938 (m-80) REVERT: R 44 LEU cc_start: 0.5898 (mm) cc_final: 0.5645 (mt) REVERT: R 123 MET cc_start: 0.4447 (mtt) cc_final: 0.3940 (mmt) REVERT: R 537 MET cc_start: 0.7472 (ttm) cc_final: 0.6970 (mtt) outliers start: 31 outliers final: 19 residues processed: 119 average time/residue: 0.4623 time to fit residues: 59.0290 Evaluate side-chains 115 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain R residue 532 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN L 80 GLN L 149 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.181000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.158249 restraints weight = 11821.865| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 1.75 r_work: 0.4477 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4361 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7306 Z= 0.153 Angle : 0.603 7.659 9950 Z= 0.317 Chirality : 0.040 0.134 1133 Planarity : 0.004 0.040 1258 Dihedral : 5.171 49.965 1016 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.66 % Allowed : 18.56 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 aren not related in a simple way. whole: 0.50 (0.28), residues: 923 helix: 1.17 (0.29), residues: 325 sheet: 0.42 (0.32), residues: 266 loop : -0.47 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.024 0.002 TYR L 92 PHE 0.040 0.002 PHE H 136 TRP 0.015 0.002 TRP H 117 HIS 0.005 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7299) covalent geometry : angle 0.60277 ( 9936) SS BOND : bond 0.00107 ( 7) SS BOND : angle 0.84576 ( 14) hydrogen bonds : bond 0.03758 ( 401) hydrogen bonds : angle 4.94004 ( 1110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.5936 (ttp-170) REVERT: H 53 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.6275 (p90) REVERT: H 155 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6889 (mt) REVERT: H 220 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7529 (mppt) REVERT: K 17 SER cc_start: 0.6330 (m) cc_final: 0.5694 (p) REVERT: L 43 LYS cc_start: 0.7243 (mttt) cc_final: 0.6030 (pttp) REVERT: L 141 PHE cc_start: 0.4292 (t80) cc_final: 0.3549 (t80) REVERT: L 211 PHE cc_start: 0.5528 (p90) cc_final: 0.4490 (p90) REVERT: R 44 LEU cc_start: 0.5908 (mm) cc_final: 0.5664 (mt) REVERT: R 123 MET cc_start: 0.4558 (mtt) cc_final: 0.4057 (mmt) REVERT: R 211 LEU cc_start: 0.7030 (tp) cc_final: 0.6793 (mt) REVERT: R 537 MET cc_start: 0.7393 (ttm) cc_final: 0.6856 (mtt) outliers start: 27 outliers final: 19 residues processed: 116 average time/residue: 0.4865 time to fit residues: 60.3141 Evaluate side-chains 117 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain R residue 532 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 139 ASN L 157 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.179459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.156629 restraints weight = 11974.845| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 1.76 r_work: 0.4455 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4342 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7306 Z= 0.176 Angle : 0.622 7.903 9950 Z= 0.327 Chirality : 0.041 0.141 1133 Planarity : 0.005 0.053 1258 Dihedral : 5.333 49.826 1016 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.20 % Allowed : 18.16 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 aren not related in a simple way. whole: 0.42 (0.28), residues: 923 helix: 1.13 (0.29), residues: 325 sheet: 0.34 (0.32), residues: 270 loop : -0.51 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.026 0.002 TYR L 92 PHE 0.038 0.002 PHE H 71 TRP 0.020 0.002 TRP H 117 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7299) covalent geometry : angle 0.62147 ( 9936) SS BOND : bond 0.00202 ( 7) SS BOND : angle 1.05536 ( 14) hydrogen bonds : bond 0.03914 ( 401) hydrogen bonds : angle 5.05969 ( 1110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: H 22 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6174 (ttp-170) REVERT: H 53 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6469 (p90) REVERT: H 220 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7613 (mppt) REVERT: L 43 LYS cc_start: 0.7268 (mttt) cc_final: 0.6016 (pttp) REVERT: L 141 PHE cc_start: 0.4269 (t80) cc_final: 0.3558 (t80) REVERT: L 142 TYR cc_start: 0.4951 (OUTLIER) cc_final: 0.3883 (m-80) REVERT: L 211 PHE cc_start: 0.5771 (p90) cc_final: 0.4709 (p90) REVERT: R 44 LEU cc_start: 0.5792 (mm) cc_final: 0.5538 (mt) REVERT: R 123 MET cc_start: 0.4625 (mtt) cc_final: 0.4093 (mmt) REVERT: R 537 MET cc_start: 0.7454 (ttm) cc_final: 0.6942 (mtt) outliers start: 31 outliers final: 18 residues processed: 116 average time/residue: 0.4396 time to fit residues: 54.7633 Evaluate side-chains 112 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain R residue 532 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.178519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.157937 restraints weight = 11915.674| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 2.07 r_work: 0.4417 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4296 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7306 Z= 0.213 Angle : 0.671 8.213 9950 Z= 0.354 Chirality : 0.042 0.152 1133 Planarity : 0.005 0.042 1258 Dihedral : 5.603 50.436 1016 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.20 % Allowed : 18.70 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 aren not related in a simple way. whole: 0.16 (0.28), residues: 923 helix: 0.95 (0.29), residues: 326 sheet: 0.23 (0.31), residues: 275 loop : -0.74 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 101 TYR 0.027 0.002 TYR L 92 PHE 0.032 0.002 PHE H 71 TRP 0.024 0.003 TRP H 117 HIS 0.003 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 7299) covalent geometry : angle 0.66979 ( 9936) SS BOND : bond 0.00326 ( 7) SS BOND : angle 1.15616 ( 14) hydrogen bonds : bond 0.04206 ( 401) hydrogen bonds : angle 5.31252 ( 1110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 22 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.5828 (ttp-170) REVERT: H 53 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.6605 (p90) REVERT: H 220 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7605 (mppt) REVERT: L 43 LYS cc_start: 0.7386 (mttt) cc_final: 0.6123 (pttp) REVERT: L 141 PHE cc_start: 0.4253 (t80) cc_final: 0.3546 (t80) REVERT: L 142 TYR cc_start: 0.5017 (OUTLIER) cc_final: 0.3757 (m-80) REVERT: L 211 PHE cc_start: 0.5746 (p90) cc_final: 0.4665 (p90) REVERT: R 44 LEU cc_start: 0.5878 (mm) cc_final: 0.5657 (mp) REVERT: R 123 MET cc_start: 0.4928 (mtt) cc_final: 0.4324 (mmt) REVERT: R 537 MET cc_start: 0.7476 (ttm) cc_final: 0.7016 (mtt) outliers start: 31 outliers final: 21 residues processed: 118 average time/residue: 0.4504 time to fit residues: 57.0824 Evaluate side-chains 111 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain R residue 532 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS R 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.179483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.156532 restraints weight = 11930.669| |-----------------------------------------------------------------------------| r_work (start): 0.4536 rms_B_bonded: 1.78 r_work: 0.4447 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4329 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7306 Z= 0.180 Angle : 0.634 7.879 9950 Z= 0.335 Chirality : 0.041 0.142 1133 Planarity : 0.005 0.043 1258 Dihedral : 5.483 52.022 1016 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.07 % Allowed : 19.92 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 aren not related in a simple way. whole: 0.22 (0.28), residues: 923 helix: 1.02 (0.29), residues: 325 sheet: 0.20 (0.32), residues: 269 loop : -0.68 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.027 0.002 TYR L 92 PHE 0.023 0.002 PHE H 71 TRP 0.023 0.002 TRP R 193 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7299) covalent geometry : angle 0.63379 ( 9936) SS BOND : bond 0.00184 ( 7) SS BOND : angle 0.97622 ( 14) hydrogen bonds : bond 0.03925 ( 401) hydrogen bonds : angle 5.16965 ( 1110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6200 (ttp-170) REVERT: H 53 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.6480 (p90) REVERT: H 220 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7585 (mppt) REVERT: L 43 LYS cc_start: 0.7320 (mttt) cc_final: 0.6066 (pttp) REVERT: L 141 PHE cc_start: 0.4131 (t80) cc_final: 0.3457 (t80) REVERT: L 142 TYR cc_start: 0.4909 (OUTLIER) cc_final: 0.3597 (m-80) REVERT: L 211 PHE cc_start: 0.5731 (p90) cc_final: 0.4637 (p90) REVERT: R 44 LEU cc_start: 0.5861 (mm) cc_final: 0.5636 (mp) REVERT: R 123 MET cc_start: 0.4939 (mtt) cc_final: 0.4408 (mmt) REVERT: R 537 MET cc_start: 0.7380 (ttm) cc_final: 0.6907 (mtt) REVERT: R 608 LYS cc_start: 0.5291 (tttt) cc_final: 0.3932 (ptmt) outliers start: 30 outliers final: 21 residues processed: 114 average time/residue: 0.4620 time to fit residues: 56.3011 Evaluate side-chains 117 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain R residue 532 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.177798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.154335 restraints weight = 11858.083| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 1.79 r_work: 0.4419 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4302 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7306 Z= 0.231 Angle : 0.703 8.724 9950 Z= 0.372 Chirality : 0.043 0.157 1133 Planarity : 0.005 0.044 1258 Dihedral : 5.778 51.679 1016 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.20 % Allowed : 20.60 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -0.11 (0.28), residues: 923 helix: 0.77 (0.29), residues: 325 sheet: 0.12 (0.31), residues: 269 loop : -0.97 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 25 TYR 0.029 0.003 TYR L 92 PHE 0.030 0.003 PHE H 71 TRP 0.030 0.003 TRP R 193 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 7299) covalent geometry : angle 0.70154 ( 9936) SS BOND : bond 0.00348 ( 7) SS BOND : angle 1.24743 ( 14) hydrogen bonds : bond 0.04354 ( 401) hydrogen bonds : angle 5.45395 ( 1110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4412.11 seconds wall clock time: 75 minutes 48.52 seconds (4548.52 seconds total)