Starting phenix.real_space_refine on Fri Dec 8 02:55:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/12_2023/8u4v_41899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/12_2023/8u4v_41899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/12_2023/8u4v_41899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/12_2023/8u4v_41899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/12_2023/8u4v_41899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4v_41899/12_2023/8u4v_41899_updated.pdb" } resolution = 2.99 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= 0.000 sd= 0.018 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 31 5.16 5 C 4212 2.51 5 N 1102 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "H GLU 252": "OE1" <-> "OE2" Residue "K GLU 44": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6637 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1324 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 970 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1735 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Conformer: "B" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} bond proxies already assigned to first conformer: 1761 Chain: "K" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.74 Number of scatterers: 6637 At special positions: 0 Unit cell: (77.964, 96.12, 129.228, 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 31 16.00 O 1292 8.00 N 1102 7.00 C 4212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 64 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 113 " distance=2.03 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 219 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 15 sheets defined 17.4% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 6 through 26 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 75 through 100 removed outlier: 3.602A pdb=" N ALA A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 148 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 162 through 182 Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 208 through 212 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 114 through 116 No H-bonds generated for 'chain 'H' and resid 114 through 116' Processing helix chain 'H' and resid 131 through 136 removed outlier: 3.588A pdb=" N LEU H 135 " --> pdb=" O TRP H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 228 No H-bonds generated for 'chain 'H' and resid 226 through 228' Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing sheet with id= A, first strand: chain 'A' and resid 31 through 35 Processing sheet with id= B, first strand: chain 'B' and resid 205 through 210 removed outlier: 3.570A pdb=" N GLU B 207 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER B 265 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS B 273 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.912A pdb=" N GLN B 249 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 285 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 29 through 32 Processing sheet with id= E, first strand: chain 'L' and resid 35 through 38 removed outlier: 6.109A pdb=" N LYS L 128 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA L 38 " --> pdb=" O LYS L 128 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU L 130 " --> pdb=" O ALA L 38 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.113A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 139 through 143 Processing sheet with id= H, first strand: chain 'L' and resid 169 through 174 Processing sheet with id= I, first strand: chain 'H' and resid 29 through 33 Processing sheet with id= J, first strand: chain 'H' and resid 147 through 149 removed outlier: 6.026A pdb=" N ARG H 64 " --> pdb=" O TRP H 73 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP H 73 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ALA H 66 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU H 71 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 123 through 126 Processing sheet with id= L, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.584A pdb=" N SER H 220 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 191 through 194 removed outlier: 4.792A pdb=" N TYR H 234 " --> pdb=" O VAL H 251 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.523A pdb=" N GLY K 16 " --> pdb=" O LEU K 86 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU K 86 " --> pdb=" O GLY K 16 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU K 18 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASN K 84 " --> pdb=" O LEU K 18 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU K 20 " --> pdb=" O GLN K 82 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLN K 82 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N CYS K 22 " --> pdb=" O TYR K 80 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR K 80 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA K 24 " --> pdb=" O THR K 78 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR K 78 " --> pdb=" O ALA K 24 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 95 through 99 removed outlier: 3.955A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 756 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: 1.77 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1464 1.33 - 1.45: 1560 1.45 - 1.57: 3717 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 6785 Sorted by residual: bond pdb=" N GLY K 10 " pdb=" CA GLY K 10 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.20e-03 1.18e+04 9.94e+00 bond pdb=" N VAL K 50 " pdb=" CA VAL K 50 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.27e+00 bond pdb=" CCJ AV0 H 301 " pdb=" OBV AV0 H 301 " ideal model delta sigma weight residual 1.374 1.431 -0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" CA SER L 35 " pdb=" CB SER L 35 " ideal model delta sigma weight residual 1.533 1.489 0.044 1.66e-02 3.63e+03 7.10e+00 bond pdb=" N ILE K 29 " pdb=" CA ILE K 29 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.35e-02 5.49e+03 7.09e+00 ... (remaining 6780 not shown) Histogram of bond angle deviations from ideal: 77.15 - 88.55: 4 88.55 - 99.95: 3 99.95 - 111.36: 3147 111.36 - 122.76: 5147 122.76 - 134.16: 930 Bond angle restraints: 9231 Sorted by residual: angle pdb=" CBR AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 110.70 77.15 33.55 3.00e+00 1.11e-01 1.25e+02 angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBS AV0 H 301 " ideal model delta sigma weight residual 110.52 81.56 28.96 3.00e+00 1.11e-01 9.32e+01 angle pdb=" C ARG K 38 " pdb=" CA ARG K 38 " pdb=" CB ARG K 38 " ideal model delta sigma weight residual 109.38 92.93 16.45 1.80e+00 3.09e-01 8.35e+01 angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBR AV0 H 301 " ideal model delta sigma weight residual 107.79 81.90 25.89 3.00e+00 1.11e-01 7.45e+01 angle pdb=" CBS AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 105.72 80.28 25.44 3.00e+00 1.11e-01 7.19e+01 ... (remaining 9226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 3780 23.10 - 46.19: 246 46.19 - 69.29: 48 69.29 - 92.38: 7 92.38 - 115.48: 8 Dihedral angle restraints: 4089 sinusoidal: 1603 harmonic: 2486 Sorted by residual: dihedral pdb=" C ARG K 38 " pdb=" N ARG K 38 " pdb=" CA ARG K 38 " pdb=" CB ARG K 38 " ideal model delta harmonic sigma weight residual -122.60 -101.94 -20.66 0 2.50e+00 1.60e-01 6.83e+01 dihedral pdb=" CB CYS H 180 " pdb=" SG CYS H 180 " pdb=" SG CYS H 236 " pdb=" CB CYS H 236 " ideal model delta sinusoidal sigma weight residual -86.00 -132.12 46.12 1 1.00e+01 1.00e-02 2.95e+01 dihedral pdb=" C ASN L 163 " pdb=" N ASN L 163 " pdb=" CA ASN L 163 " pdb=" CB ASN L 163 " ideal model delta harmonic sigma weight residual -122.60 -134.49 11.89 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 4086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 985 0.111 - 0.222: 65 0.222 - 0.332: 4 0.332 - 0.443: 1 0.443 - 0.554: 1 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA ASN L 163 " pdb=" N ASN L 163 " pdb=" C ASN L 163 " pdb=" CB ASN L 163 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CA ARG K 38 " pdb=" N ARG K 38 " pdb=" C ARG K 38 " pdb=" CB ARG K 38 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA LYS A 157 " pdb=" N LYS A 157 " pdb=" C LYS A 157 " pdb=" CB LYS A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1053 not shown) Planarity restraints: 1153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 73 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO A 74 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 111 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" CD GLU A 111 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU A 111 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 111 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 184 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C SER L 184 " 0.027 2.00e-02 2.50e+03 pdb=" O SER L 184 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN L 185 " -0.009 2.00e-02 2.50e+03 ... (remaining 1150 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 109 2.63 - 3.20: 5789 3.20 - 3.77: 10316 3.77 - 4.33: 14711 4.33 - 4.90: 24704 Nonbonded interactions: 55629 Sorted by model distance: nonbonded pdb=" O THR H 171 " pdb=" OG1 THR H 175 " model vdw 2.063 2.440 nonbonded pdb=" OG SER L 51 " pdb=" OE1 GLN L 52 " model vdw 2.199 2.440 nonbonded pdb=" O ALA L 178 " pdb=" NE2 GLN L 180 " model vdw 2.287 2.520 nonbonded pdb=" CBS AV0 H 301 " pdb=" OBV AV0 H 301 " model vdw 2.334 2.752 nonbonded pdb=" O SER L 119 " pdb=" OG SER H 85 " model vdw 2.354 2.440 ... (remaining 55624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.810 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.930 Find NCS groups from input model: 0.350 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:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.006 0.057 6785 Z= 0.385 Angle : 1.121 33.548 9231 Z= 0.618 Chirality : 0.060 0.554 1056 Planarity : 0.004 0.060 1153 Dihedral : 16.562 115.481 2483 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.83 % Allowed : 21.47 % Favored : 77.70 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 12.50 % 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: 0.66 (0.30), residues: 853 helix: 2.16 (0.43), residues: 139 sheet: 0.22 (0.29), residues: 344 loop : 0.13 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 PHE 0.013 0.001 PHE K 37 TYR 0.007 0.001 TYR H 121 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.750 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 149 average time/residue: 1.1971 time to fit residues: 187.3738 Evaluate side-chains 114 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0671 time to fit residues: 1.0280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN L 115 GLN L 162 ASN ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 GLN H 211 GLN K 3 GLN K 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6785 Z= 0.214 Angle : 0.886 31.873 9231 Z= 0.365 Chirality : 0.042 0.162 1056 Planarity : 0.004 0.050 1153 Dihedral : 8.886 90.072 1052 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.02 % Allowed : 20.50 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.08 (0.30), residues: 853 helix: 2.39 (0.42), residues: 139 sheet: 0.53 (0.29), residues: 350 loop : 0.39 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.001 0.000 HIS H 61 PHE 0.011 0.001 PHE B 261 TYR 0.011 0.001 TYR B 264 ARG 0.004 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 0.791 Fit side-chains outliers start: 29 outliers final: 10 residues processed: 133 average time/residue: 1.1763 time to fit residues: 164.7051 Evaluate side-chains 121 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 3 residues processed: 7 average time/residue: 0.1297 time to fit residues: 2.1344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 21 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 0.0270 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6785 Z= 0.170 Angle : 0.855 32.363 9231 Z= 0.347 Chirality : 0.041 0.142 1056 Planarity : 0.004 0.051 1153 Dihedral : 7.116 90.789 1052 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.63 % Allowed : 22.44 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.27 (0.30), residues: 853 helix: 2.50 (0.43), residues: 140 sheet: 0.74 (0.29), residues: 331 loop : 0.44 (0.35), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 PHE 0.009 0.001 PHE K 37 TYR 0.009 0.001 TYR B 264 ARG 0.004 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.667 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 118 average time/residue: 1.2324 time to fit residues: 152.7307 Evaluate side-chains 108 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.2097 time to fit residues: 1.8827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6785 Z= 0.200 Angle : 0.845 31.924 9231 Z= 0.343 Chirality : 0.041 0.142 1056 Planarity : 0.004 0.052 1153 Dihedral : 7.041 91.411 1052 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.46 % Allowed : 21.88 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.34 (0.31), residues: 853 helix: 2.59 (0.44), residues: 139 sheet: 0.71 (0.28), residues: 353 loop : 0.55 (0.37), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 PHE 0.010 0.001 PHE B 261 TYR 0.011 0.001 TYR L 217 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.708 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 114 average time/residue: 1.1845 time to fit residues: 141.9890 Evaluate side-chains 113 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 7 average time/residue: 0.2305 time to fit residues: 2.9059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.0060 chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6785 Z= 0.187 Angle : 0.845 31.819 9231 Z= 0.342 Chirality : 0.040 0.143 1056 Planarity : 0.003 0.043 1153 Dihedral : 7.037 92.307 1052 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.35 % Allowed : 23.41 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.38 (0.31), residues: 853 helix: 2.62 (0.44), residues: 139 sheet: 0.76 (0.28), residues: 353 loop : 0.54 (0.37), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 PHE 0.009 0.001 PHE B 261 TYR 0.013 0.001 TYR A 67 ARG 0.002 0.000 ARG L 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.798 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 115 average time/residue: 1.2465 time to fit residues: 150.6495 Evaluate side-chains 111 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 4 average time/residue: 0.4308 time to fit residues: 2.9121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6785 Z= 0.261 Angle : 0.855 31.789 9231 Z= 0.351 Chirality : 0.041 0.143 1056 Planarity : 0.004 0.039 1153 Dihedral : 7.141 92.254 1052 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 23.41 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.37 (0.30), residues: 853 helix: 2.56 (0.44), residues: 139 sheet: 0.77 (0.28), residues: 352 loop : 0.54 (0.37), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 125 HIS 0.002 0.000 HIS H 127 PHE 0.013 0.001 PHE B 261 TYR 0.013 0.001 TYR L 217 ARG 0.004 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.813 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 115 average time/residue: 1.2383 time to fit residues: 149.5696 Evaluate side-chains 111 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.6476 time to fit residues: 4.3877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6785 Z= 0.275 Angle : 0.871 31.745 9231 Z= 0.357 Chirality : 0.042 0.161 1056 Planarity : 0.003 0.039 1153 Dihedral : 7.203 92.646 1052 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.19 % Allowed : 22.85 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.36 (0.30), residues: 853 helix: 2.54 (0.44), residues: 136 sheet: 0.76 (0.28), residues: 351 loop : 0.55 (0.36), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 125 HIS 0.002 0.000 HIS H 127 PHE 0.012 0.001 PHE B 261 TYR 0.011 0.001 TYR B 264 ARG 0.004 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.746 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 117 average time/residue: 1.2064 time to fit residues: 148.4918 Evaluate side-chains 110 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.4591 time to fit residues: 2.4347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 51 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 0.0370 chunk 77 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6785 Z= 0.146 Angle : 0.837 31.618 9231 Z= 0.337 Chirality : 0.040 0.143 1056 Planarity : 0.003 0.039 1153 Dihedral : 7.058 92.184 1052 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.63 % Allowed : 23.13 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.46 (0.30), residues: 853 helix: 2.72 (0.44), residues: 136 sheet: 0.84 (0.28), residues: 350 loop : 0.56 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 PHE 0.008 0.001 PHE B 316 TYR 0.012 0.001 TYR K 60 ARG 0.005 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.794 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 119 average time/residue: 1.1588 time to fit residues: 145.2738 Evaluate side-chains 112 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1435 time to fit residues: 1.8250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN K 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6785 Z= 0.291 Angle : 0.886 31.714 9231 Z= 0.365 Chirality : 0.042 0.175 1056 Planarity : 0.004 0.040 1153 Dihedral : 7.179 91.791 1052 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.94 % Allowed : 24.10 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.39 (0.30), residues: 853 helix: 2.52 (0.44), residues: 136 sheet: 0.83 (0.28), residues: 347 loop : 0.55 (0.36), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.002 0.000 HIS H 127 PHE 0.014 0.001 PHE B 261 TYR 0.012 0.001 TYR L 217 ARG 0.004 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.696 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 1.2718 time to fit residues: 148.2280 Evaluate side-chains 109 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0624 time to fit residues: 1.1180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.0470 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN K 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6785 Z= 0.283 Angle : 0.880 31.670 9231 Z= 0.362 Chirality : 0.042 0.144 1056 Planarity : 0.004 0.039 1153 Dihedral : 7.189 91.806 1052 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.94 % Allowed : 24.24 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.38 (0.30), residues: 853 helix: 2.49 (0.44), residues: 136 sheet: 0.79 (0.28), residues: 348 loop : 0.58 (0.36), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 PHE 0.013 0.001 PHE B 261 TYR 0.011 0.001 TYR L 217 ARG 0.004 0.000 ARG K 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.770 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 1.2850 time to fit residues: 149.7769 Evaluate side-chains 106 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 0.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN K 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.067736 restraints weight = 14390.114| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.41 r_work: 0.2604 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6785 Z= 0.216 Angle : 0.876 31.604 9231 Z= 0.359 Chirality : 0.041 0.154 1056 Planarity : 0.003 0.039 1153 Dihedral : 7.142 91.724 1052 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.80 % Allowed : 24.65 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.37 (0.30), residues: 853 helix: 2.56 (0.44), residues: 136 sheet: 0.81 (0.28), residues: 350 loop : 0.51 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 PHE 0.010 0.001 PHE B 261 TYR 0.010 0.001 TYR A 67 ARG 0.004 0.000 ARG K 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.63 seconds wall clock time: 61 minutes 3.91 seconds (3663.91 seconds total)