Starting phenix.real_space_refine on Fri Jul 25 06:39:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hb3_52012/07_2025/9hb3_52012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hb3_52012/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hb3_52012/07_2025/9hb3_52012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hb3_52012/07_2025/9hb3_52012.map" model { file = "/net/cci-nas-00/data/ceres_data/9hb3_52012/07_2025/9hb3_52012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hb3_52012/07_2025/9hb3_52012.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 1, 'ASN:plan1': 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: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 103 Time building chain proxies: 5.09, per 1000 atoms: 0.71 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: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.12 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: 2.53 Time building geometry restraints manager: 2.01 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.540 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- 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 : 8.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP H 117 HIS 0.003 0.001 HIS L 200 PHE 0.017 0.002 PHE R 287 TYR 0.015 0.002 TYR L 92 ARG 0.006 0.000 ARG R 104 Details of bonding type rmsd hydrogen bonds : bond 0.08466 ( 401) hydrogen bonds : angle 6.19355 ( 1110) SS BOND : bond 0.00199 ( 7) SS BOND : angle 0.92858 ( 14) covalent geometry : bond 0.00409 ( 7299) covalent geometry : angle 0.64523 ( 9936) *********************** 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 : 0.782 Fit side-chains REVERT: H 90 ARG cc_start: 0.3421 (mtt180) cc_final: 0.3087 (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: 1.0973 time to fit residues: 176.6281 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 : 0.712 ------------------------------------------------------------------------------- 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 78 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 178 HIS 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 = 0.4868 r_free = 0.4868 target = 0.187813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.164569 restraints weight = 11794.020| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 1.74 r_work: 0.4454 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4334 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7306 Z= 0.245 Angle : 0.707 7.857 9950 Z= 0.377 Chirality : 0.044 0.160 1133 Planarity : 0.006 0.074 1258 Dihedral : 5.747 43.457 1017 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.07 % Allowed : 10.03 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.28), residues: 923 helix: 0.66 (0.28), residues: 326 sheet: 0.30 (0.29), residues: 288 loop : -0.16 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 117 HIS 0.004 0.001 HIS H 38 PHE 0.021 0.003 PHE H 71 TYR 0.017 0.003 TYR L 87 ARG 0.008 0.001 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 401) hydrogen bonds : angle 5.54777 ( 1110) SS BOND : bond 0.00728 ( 7) SS BOND : angle 1.46131 ( 14) covalent geometry : bond 0.00546 ( 7299) covalent geometry : angle 0.70540 ( 9936) *********************** 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 145 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.784 Fit side-chains REVERT: H 53 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6320 (p90) REVERT: H 219 THR cc_start: 0.7449 (m) cc_final: 0.7187 (m) REVERT: H 220 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7323 (mtmm) REVERT: L 43 LYS cc_start: 0.7098 (mttt) cc_final: 0.5916 (pttp) REVERT: L 141 PHE cc_start: 0.4715 (t80) cc_final: 0.3957 (t80) REVERT: L 157 GLN cc_start: 0.5380 (mm-40) cc_final: 0.4207 (mm110) REVERT: R 123 MET cc_start: 0.4363 (mtt) cc_final: 0.3699 (mmt) outliers start: 30 outliers final: 14 residues processed: 135 average time/residue: 0.9277 time to fit residues: 134.1886 Evaluate side-chains 108 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 86 THR 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 40 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.188365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.165308 restraints weight = 11886.695| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 1.74 r_work: 0.4474 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4357 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7306 Z= 0.163 Angle : 0.611 9.111 9950 Z= 0.317 Chirality : 0.041 0.178 1133 Planarity : 0.005 0.043 1258 Dihedral : 5.252 45.882 1016 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.20 % Allowed : 12.87 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.28), residues: 923 helix: 0.93 (0.28), residues: 324 sheet: 0.40 (0.30), residues: 279 loop : -0.19 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 117 HIS 0.004 0.001 HIS H 38 PHE 0.017 0.002 PHE H 71 TYR 0.025 0.002 TYR L 92 ARG 0.003 0.000 ARG K 31 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 401) hydrogen bonds : angle 5.13086 ( 1110) SS BOND : bond 0.00265 ( 7) SS BOND : angle 1.09239 ( 14) covalent geometry : bond 0.00359 ( 7299) covalent geometry : angle 0.61034 ( 9936) *********************** 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 139 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.740 Fit side-chains REVERT: H 53 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6257 (p90) REVERT: H 219 THR cc_start: 0.7292 (m) cc_final: 0.7065 (m) REVERT: H 220 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7670 (mppt) REVERT: L 43 LYS cc_start: 0.7041 (mttt) cc_final: 0.5837 (pttp) REVERT: L 141 PHE cc_start: 0.4594 (t80) cc_final: 0.3815 (t80) REVERT: L 157 GLN cc_start: 0.5376 (mm-40) cc_final: 0.4353 (mm-40) REVERT: R 123 MET cc_start: 0.4763 (mtt) cc_final: 0.4067 (mmt) REVERT: R 221 ILE cc_start: 0.7054 (tt) cc_final: 0.6846 (tp) REVERT: R 564 ASP cc_start: 0.4742 (m-30) cc_final: 0.4329 (t70) outliers start: 31 outliers final: 15 residues processed: 126 average time/residue: 0.9068 time to fit residues: 122.9399 Evaluate side-chains 110 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 218 ASN 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 160 ASN 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 7 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN H 213 ASN L 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.178506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.154698 restraints weight = 11851.686| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 1.77 r_work: 0.4416 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4295 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 7306 Z= 0.252 Angle : 0.711 9.036 9950 Z= 0.379 Chirality : 0.044 0.162 1133 Planarity : 0.005 0.055 1258 Dihedral : 5.711 43.305 1016 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.47 % Allowed : 15.99 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 923 helix: 0.58 (0.28), residues: 320 sheet: 0.12 (0.31), residues: 274 loop : -0.54 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 117 HIS 0.004 0.001 HIS H 38 PHE 0.014 0.002 PHE R 565 TYR 0.027 0.003 TYR L 92 ARG 0.004 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 401) hydrogen bonds : angle 5.62415 ( 1110) SS BOND : bond 0.00259 ( 7) SS BOND : angle 1.44126 ( 14) covalent geometry : bond 0.00563 ( 7299) covalent geometry : angle 0.70941 ( 9936) *********************** 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 134 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.702 Fit side-chains REVERT: H 53 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.6552 (p90) REVERT: H 220 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7516 (mtmm) REVERT: L 43 LYS cc_start: 0.7321 (mttt) cc_final: 0.6057 (pttp) REVERT: L 141 PHE cc_start: 0.4536 (t80) cc_final: 0.3878 (t80) REVERT: L 142 TYR cc_start: 0.4918 (OUTLIER) cc_final: 0.4013 (m-80) REVERT: R 123 MET cc_start: 0.4735 (mtt) cc_final: 0.4444 (mmt) REVERT: R 221 ILE cc_start: 0.7026 (tt) cc_final: 0.6798 (tp) REVERT: R 562 MET cc_start: -0.0804 (OUTLIER) cc_final: -0.2525 (mtt) outliers start: 33 outliers final: 23 residues processed: 121 average time/residue: 0.9333 time to fit residues: 121.0219 Evaluate side-chains 117 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 218 ASN Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 17 SER 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 19 ARG 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 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 160 VAL 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 15 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN L 157 GLN L 160 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.180660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.157589 restraints weight = 11904.980| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 1.74 r_work: 0.4454 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4338 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.4421 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= 0.170 Angle : 0.616 8.100 9950 Z= 0.323 Chirality : 0.041 0.138 1133 Planarity : 0.004 0.044 1258 Dihedral : 5.333 47.600 1016 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.88 % Allowed : 16.40 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 923 helix: 0.81 (0.28), residues: 324 sheet: 0.17 (0.31), residues: 276 loop : -0.46 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 117 HIS 0.004 0.001 HIS R 567 PHE 0.030 0.002 PHE H 136 TYR 0.024 0.002 TYR L 92 ARG 0.005 0.000 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 401) hydrogen bonds : angle 5.22225 ( 1110) SS BOND : bond 0.00189 ( 7) SS BOND : angle 1.05455 ( 14) covalent geometry : bond 0.00382 ( 7299) covalent geometry : angle 0.61563 ( 9936) *********************** 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 136 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.6331 (p90) REVERT: H 220 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7591 (mppt) REVERT: L 43 LYS cc_start: 0.7264 (mttt) cc_final: 0.6047 (pttp) REVERT: L 142 TYR cc_start: 0.4863 (OUTLIER) cc_final: 0.3522 (m-80) REVERT: R 44 LEU cc_start: 0.5934 (mm) cc_final: 0.5674 (mt) REVERT: R 123 MET cc_start: 0.4832 (mtt) cc_final: 0.4112 (mmt) REVERT: R 211 LEU cc_start: 0.6991 (tp) cc_final: 0.6749 (mt) REVERT: R 221 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6998 (tp) REVERT: R 537 MET cc_start: 0.7447 (ttm) cc_final: 0.6948 (mtt) REVERT: R 564 ASP cc_start: 0.4643 (m-30) cc_final: 0.4372 (t70) REVERT: R 608 LYS cc_start: 0.4997 (tttt) cc_final: 0.3638 (ptmt) outliers start: 36 outliers final: 19 residues processed: 122 average time/residue: 1.0099 time to fit residues: 132.3649 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 : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR 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 73 ILE 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 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 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 221 ILE Chi-restraints excluded: chain R residue 504 LEU 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 87 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 139 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.180901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.160039 restraints weight = 11817.003| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 2.11 r_work: 0.4431 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4309 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7306 Z= 0.166 Angle : 0.614 8.040 9950 Z= 0.321 Chirality : 0.041 0.138 1133 Planarity : 0.005 0.056 1258 Dihedral : 5.238 48.090 1016 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.88 % Allowed : 16.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 923 helix: 1.04 (0.29), residues: 324 sheet: 0.26 (0.32), residues: 270 loop : -0.43 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 117 HIS 0.006 0.001 HIS L 200 PHE 0.039 0.002 PHE H 136 TYR 0.024 0.002 TYR L 92 ARG 0.004 0.000 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 401) hydrogen bonds : angle 5.12520 ( 1110) SS BOND : bond 0.00171 ( 7) SS BOND : angle 0.95632 ( 14) covalent geometry : bond 0.00374 ( 7299) covalent geometry : angle 0.61343 ( 9936) *********************** 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 136 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.6208 (p90) REVERT: H 220 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7661 (mppt) REVERT: L 141 PHE cc_start: 0.4335 (t80) cc_final: 0.3626 (t80) REVERT: L 142 TYR cc_start: 0.4938 (OUTLIER) cc_final: 0.3537 (m-80) REVERT: R 44 LEU cc_start: 0.5923 (mm) cc_final: 0.5678 (mt) REVERT: R 123 MET cc_start: 0.4909 (mtt) cc_final: 0.4258 (mmt) REVERT: R 537 MET cc_start: 0.7438 (ttm) cc_final: 0.6950 (mtt) REVERT: R 608 LYS cc_start: 0.4855 (tttt) cc_final: 0.3602 (ptmt) outliers start: 36 outliers final: 22 residues processed: 127 average time/residue: 1.0226 time to fit residues: 140.1488 Evaluate side-chains 116 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 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 38 ARG 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 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 221 ILE Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain R residue 532 ASP Chi-restraints excluded: chain R residue 573 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 0.0070 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN L 4 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.183007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.162487 restraints weight = 11804.070| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 2.20 r_work: 0.4476 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4356 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7306 Z= 0.125 Angle : 0.592 10.193 9950 Z= 0.303 Chirality : 0.040 0.124 1133 Planarity : 0.004 0.039 1258 Dihedral : 5.034 50.991 1016 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.20 % Allowed : 18.29 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 923 helix: 1.34 (0.29), residues: 324 sheet: 0.43 (0.33), residues: 260 loop : -0.38 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 193 HIS 0.007 0.001 HIS L 200 PHE 0.033 0.002 PHE H 136 TYR 0.022 0.001 TYR L 92 ARG 0.004 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 401) hydrogen bonds : angle 4.74467 ( 1110) SS BOND : bond 0.00101 ( 7) SS BOND : angle 0.74021 ( 14) covalent geometry : bond 0.00274 ( 7299) covalent geometry : angle 0.59145 ( 9936) *********************** 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 135 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.6225 (p90) REVERT: H 86 MET cc_start: 0.6266 (mpp) cc_final: 0.5572 (mmt) REVERT: H 116 TYR cc_start: 0.7128 (m-80) cc_final: 0.6763 (m-80) REVERT: H 220 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7692 (mppt) REVERT: K 17 SER cc_start: 0.6150 (m) cc_final: 0.5640 (p) REVERT: L 157 GLN cc_start: 0.5312 (mm110) cc_final: 0.4063 (mm-40) REVERT: L 211 PHE cc_start: 0.5601 (p90) cc_final: 0.4590 (p90) REVERT: R 44 LEU cc_start: 0.5806 (mm) cc_final: 0.5562 (mt) REVERT: R 123 MET cc_start: 0.4939 (mtt) cc_final: 0.4296 (mmt) REVERT: R 211 LEU cc_start: 0.6918 (tp) cc_final: 0.6685 (mt) REVERT: R 537 MET cc_start: 0.7264 (ttm) cc_final: 0.6835 (mtt) REVERT: R 608 LYS cc_start: 0.4853 (tttt) cc_final: 0.3566 (ptmt) outliers start: 31 outliers final: 16 residues processed: 126 average time/residue: 1.3508 time to fit residues: 182.4302 Evaluate side-chains 118 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 53 TYR Chi-restraints excluded: chain H residue 73 ILE 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 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 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 221 ILE 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 71 optimal weight: 0.0040 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 52 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.4572 ------------------------------------------------------------------------------- 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 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.183058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.162580 restraints weight = 11885.521| |-----------------------------------------------------------------------------| r_work (start): 0.4613 rms_B_bonded: 2.12 r_work: 0.4487 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4366 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7306 Z= 0.127 Angle : 0.595 10.437 9950 Z= 0.304 Chirality : 0.040 0.126 1133 Planarity : 0.005 0.060 1258 Dihedral : 4.939 51.174 1016 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.85 % Allowed : 19.78 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 923 helix: 1.39 (0.29), residues: 325 sheet: 0.55 (0.33), residues: 260 loop : -0.41 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 193 HIS 0.005 0.001 HIS L 200 PHE 0.034 0.002 PHE H 71 TYR 0.023 0.002 TYR L 92 ARG 0.014 0.001 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 401) hydrogen bonds : angle 4.65114 ( 1110) SS BOND : bond 0.00077 ( 7) SS BOND : angle 0.77163 ( 14) covalent geometry : bond 0.00280 ( 7299) covalent geometry : angle 0.59451 ( 9936) *********************** 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 118 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 PRO cc_start: 0.7681 (Cg_exo) cc_final: 0.7201 (Cg_endo) REVERT: H 53 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.6072 (p90) REVERT: H 220 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7720 (mppt) REVERT: K 17 SER cc_start: 0.6114 (m) cc_final: 0.5636 (p) REVERT: L 141 PHE cc_start: 0.4235 (t80) cc_final: 0.3530 (t80) REVERT: L 157 GLN cc_start: 0.5389 (mm-40) cc_final: 0.4187 (mm-40) REVERT: L 211 PHE cc_start: 0.5601 (p90) cc_final: 0.4617 (p90) REVERT: R 44 LEU cc_start: 0.5790 (mm) cc_final: 0.5546 (mt) REVERT: R 123 MET cc_start: 0.5194 (mtt) cc_final: 0.4957 (mmt) REVERT: R 211 LEU cc_start: 0.6920 (tp) cc_final: 0.6653 (mt) REVERT: R 537 MET cc_start: 0.7283 (ttm) cc_final: 0.6881 (mtt) REVERT: R 608 LYS cc_start: 0.4815 (tttt) cc_final: 0.3598 (ptmt) outliers start: 21 outliers final: 14 residues processed: 113 average time/residue: 2.4876 time to fit residues: 291.9167 Evaluate side-chains 113 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 53 TYR Chi-restraints excluded: chain H residue 73 ILE 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 L residue 116 SER Chi-restraints excluded: chain L residue 123 SER 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 221 ILE 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 10 optimal weight: 0.0070 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN L 149 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** 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 = 0.4826 r_free = 0.4826 target = 0.179606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.158666 restraints weight = 11868.667| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 2.14 r_work: 0.4406 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4282 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7306 Z= 0.208 Angle : 0.690 10.277 9950 Z= 0.359 Chirality : 0.043 0.150 1133 Planarity : 0.005 0.044 1258 Dihedral : 5.428 49.651 1016 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.79 % Allowed : 19.65 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.28), residues: 923 helix: 1.07 (0.29), residues: 325 sheet: 0.34 (0.32), residues: 265 loop : -0.67 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 117 HIS 0.005 0.001 HIS L 200 PHE 0.028 0.002 PHE H 71 TYR 0.028 0.002 TYR L 92 ARG 0.007 0.001 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 401) hydrogen bonds : angle 5.14301 ( 1110) SS BOND : bond 0.00218 ( 7) SS BOND : angle 1.19387 ( 14) covalent geometry : bond 0.00470 ( 7299) covalent geometry : angle 0.68910 ( 9936) *********************** 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 119 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.6037 (p90) REVERT: H 220 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7739 (mppt) REVERT: L 12 LEU cc_start: 0.5400 (tt) cc_final: 0.5051 (tp) REVERT: L 141 PHE cc_start: 0.4405 (t80) cc_final: 0.3647 (t80) REVERT: L 157 GLN cc_start: 0.5088 (mm-40) cc_final: 0.4062 (mm-40) REVERT: R 44 LEU cc_start: 0.5776 (mm) cc_final: 0.5532 (mp) REVERT: R 123 MET cc_start: 0.5300 (mtt) cc_final: 0.5025 (mmt) REVERT: R 211 LEU cc_start: 0.6932 (tp) cc_final: 0.6647 (mt) REVERT: R 537 MET cc_start: 0.7503 (ttm) cc_final: 0.7015 (mtt) REVERT: R 562 MET cc_start: -0.0380 (OUTLIER) cc_final: -0.1931 (mtt) REVERT: R 608 LYS cc_start: 0.4937 (tttt) cc_final: 0.3589 (ptmt) outliers start: 28 outliers final: 19 residues processed: 110 average time/residue: 0.8240 time to fit residues: 97.9062 Evaluate side-chains 109 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 53 TYR Chi-restraints excluded: chain H residue 72 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 38 ARG Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 20 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 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain R residue 532 ASP Chi-restraints excluded: chain R residue 562 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 139 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 291 GLN R 510 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.180722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.160480 restraints weight = 12085.980| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 2.06 r_work: 0.4443 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4324 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7306 Z= 0.162 Angle : 0.640 10.042 9950 Z= 0.332 Chirality : 0.041 0.138 1133 Planarity : 0.005 0.041 1258 Dihedral : 5.247 51.906 1016 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.25 % Allowed : 20.60 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.28), residues: 923 helix: 1.24 (0.29), residues: 325 sheet: 0.36 (0.32), residues: 259 loop : -0.60 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 193 HIS 0.005 0.001 HIS L 200 PHE 0.048 0.002 PHE H 136 TYR 0.027 0.002 TYR L 92 ARG 0.008 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 401) hydrogen bonds : angle 4.95382 ( 1110) SS BOND : bond 0.00126 ( 7) SS BOND : angle 0.96267 ( 14) covalent geometry : bond 0.00360 ( 7299) covalent geometry : angle 0.63980 ( 9936) ********************** 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 116 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 PRO cc_start: 0.7883 (Cg_exo) cc_final: 0.7403 (Cg_endo) REVERT: H 53 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6069 (p90) REVERT: H 220 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7739 (mppt) REVERT: L 12 LEU cc_start: 0.5520 (tt) cc_final: 0.5190 (tp) REVERT: L 141 PHE cc_start: 0.4409 (t80) cc_final: 0.3672 (t80) REVERT: L 211 PHE cc_start: 0.5326 (p90) cc_final: 0.4372 (p90) REVERT: R 44 LEU cc_start: 0.5848 (mm) cc_final: 0.5612 (mp) REVERT: R 104 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5891 (pmt-80) REVERT: R 123 MET cc_start: 0.5303 (mtt) cc_final: 0.5030 (mmt) REVERT: R 537 MET cc_start: 0.7392 (ttm) cc_final: 0.6945 (mtt) REVERT: R 608 LYS cc_start: 0.4921 (tttt) cc_final: 0.3594 (ptmt) outliers start: 24 outliers final: 17 residues processed: 110 average time/residue: 0.8653 time to fit residues: 103.0905 Evaluate side-chains 111 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 53 TYR Chi-restraints excluded: chain H residue 72 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 38 ARG Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 20 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 168 GLN Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 221 ILE 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 88 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 chunk 82 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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** ** L 200 HIS ** 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 = 0.4850 r_free = 0.4850 target = 0.181407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.158545 restraints weight = 11883.414| |-----------------------------------------------------------------------------| r_work (start): 0.4559 rms_B_bonded: 1.76 r_work: 0.4476 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4362 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7306 Z= 0.147 Angle : 0.626 10.494 9950 Z= 0.323 Chirality : 0.041 0.160 1133 Planarity : 0.005 0.041 1258 Dihedral : 5.165 52.774 1016 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.98 % Allowed : 20.87 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.28), residues: 923 helix: 1.31 (0.29), residues: 325 sheet: 0.38 (0.32), residues: 259 loop : -0.59 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 193 HIS 0.005 0.001 HIS L 200 PHE 0.021 0.002 PHE H 71 TYR 0.026 0.002 TYR L 92 ARG 0.008 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 401) hydrogen bonds : angle 4.88336 ( 1110) SS BOND : bond 0.00115 ( 7) SS BOND : angle 0.91459 ( 14) covalent geometry : bond 0.00327 ( 7299) covalent geometry : angle 0.62501 ( 9936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9861.51 seconds wall clock time: 174 minutes 45.37 seconds (10485.37 seconds total)