Starting phenix.real_space_refine on Fri May 9 14:29:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j28_35947/05_2025/8j28_35947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j28_35947/05_2025/8j28_35947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j28_35947/05_2025/8j28_35947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j28_35947/05_2025/8j28_35947.map" model { file = "/net/cci-nas-00/data/ceres_data/8j28_35947/05_2025/8j28_35947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j28_35947/05_2025/8j28_35947.cif" } resolution = 3.7 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= 0.001 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 9 5.16 5 C 1572 2.51 5 N 441 2.21 5 O 474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2499 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 147 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "C" Number of atoms: 2047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 267, 2035 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2048 Chain: "E" Number of atoms: 140 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Conformer: "B" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} bond proxies already assigned to first conformer: 115 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR C 72 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 72 " occ=0.50 residue: pdb=" N ATYR E 72 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 72 " occ=0.50 Time building chain proxies: 3.26, per 1000 atoms: 1.30 Number of scatterers: 2499 At special positions: 0 Unit cell: (74.2, 68.9, 78.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 3 15.00 O 474 8.00 N 441 7.00 C 1572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 570.7 milliseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP C 802 " Number of C-beta restraints generated: 584 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 56.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'F' and resid 72 through 77 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.624A pdb=" N LYS C 12 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 52 removed outlier: 3.601A pdb=" N GLY C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 77 removed outlier: 3.553A pdb=" N LEU C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 91 through 114 removed outlier: 4.226A pdb=" N SER C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.898A pdb=" N PHE C 128 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.813A pdb=" N LYS C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 238 through 251 removed outlier: 4.193A pdb=" N LYS C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 Processing helix chain 'E' and resid 72 through 78 Processing helix chain 'E' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'C' and resid 118 through 123 removed outlier: 3.670A pdb=" N ALA C 119 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 152 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 121 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN C 154 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 123 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL C 55 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N PHE C 153 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 57 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLU C 155 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N SER C 59 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 191 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 257 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 256 " --> pdb=" O PHE C 280 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 409 1.31 - 1.44: 662 1.44 - 1.56: 1444 1.56 - 1.69: 4 1.69 - 1.82: 16 Bond restraints: 2535 Sorted by residual: bond pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " ideal model delta sigma weight residual 1.798 1.648 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD RGP C 802 " pdb=" OE2 RGP C 802 " ideal model delta sigma weight residual 1.302 1.397 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" N ARG C 67 " pdb=" CA ARG C 67 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" CA LEU C 65 " pdb=" C LEU C 65 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.36e-02 5.41e+03 8.67e+00 bond pdb=" CA LEU E 83 " pdb=" C LEU E 83 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.39e-02 5.18e+03 6.34e+00 ... (remaining 2530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 3315 2.36 - 4.72: 81 4.72 - 7.09: 17 7.09 - 9.45: 5 9.45 - 11.81: 1 Bond angle restraints: 3419 Sorted by residual: angle pdb=" N LEU C 65 " pdb=" CA LEU C 65 " pdb=" C LEU C 65 " ideal model delta sigma weight residual 111.71 103.48 8.23 1.15e+00 7.56e-01 5.12e+01 angle pdb=" N LEU E 83 " pdb=" CA LEU E 83 " pdb=" C LEU E 83 " ideal model delta sigma weight residual 111.75 103.06 8.69 1.28e+00 6.10e-01 4.61e+01 angle pdb=" N VAL C 25 " pdb=" CA VAL C 25 " pdb=" C VAL C 25 " ideal model delta sigma weight residual 113.42 108.56 4.86 1.17e+00 7.31e-01 1.72e+01 angle pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " pdb=" OA3 RGP C 802 " ideal model delta sigma weight residual 97.78 109.59 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N ARG C 67 " pdb=" CA ARG C 67 " pdb=" C ARG C 67 " ideal model delta sigma weight residual 111.11 106.67 4.44 1.20e+00 6.94e-01 1.37e+01 ... (remaining 3414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.27: 1458 33.27 - 66.54: 60 66.54 - 99.80: 5 99.80 - 133.07: 1 133.07 - 166.33: 1 Dihedral angle restraints: 1525 sinusoidal: 618 harmonic: 907 Sorted by residual: dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 106.33 -166.33 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP C 801 " pdb=" O5' ADP C 801 " pdb=" PA ADP C 801 " pdb=" O2A ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 40.34 -100.34 1 2.00e+01 2.50e-03 2.83e+01 dihedral pdb=" CA GLU C 220 " pdb=" C GLU C 220 " pdb=" N LYS C 221 " pdb=" CA LYS C 221 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 1522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 231 0.031 - 0.061: 103 0.061 - 0.092: 29 0.092 - 0.122: 22 0.122 - 0.153: 5 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA GLN C 68 " pdb=" N GLN C 68 " pdb=" C GLN C 68 " pdb=" CB GLN C 68 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE C 56 " pdb=" N ILE C 56 " pdb=" C ILE C 56 " pdb=" CB ILE C 56 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE C 150 " pdb=" N ILE C 150 " pdb=" C ILE C 150 " pdb=" CB ILE C 150 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 387 not shown) Planarity restraints: 431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BTYR C 72 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C BTYR C 72 " 0.067 2.00e-02 2.50e+03 pdb=" O BTYR C 72 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG C 73 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 71 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ARG C 71 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG C 71 " 0.023 2.00e-02 2.50e+03 pdb=" N ATYR C 72 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATYR C 72 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C ATYR C 72 " 0.062 2.00e-02 2.50e+03 pdb=" O ATYR C 72 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG C 73 " -0.021 2.00e-02 2.50e+03 ... (remaining 428 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 368 2.75 - 3.29: 2499 3.29 - 3.83: 3975 3.83 - 4.36: 4469 4.36 - 4.90: 7524 Nonbonded interactions: 18835 Sorted by model distance: nonbonded pdb=" OE2 GLU C 199 " pdb=" OH TYR C 202 " model vdw 2.213 3.040 nonbonded pdb=" OG SER C 60 " pdb=" OD1 ASN C 176 " model vdw 2.223 3.040 nonbonded pdb=" N GLU C 199 " pdb=" OE1 GLU C 199 " model vdw 2.252 3.120 nonbonded pdb=" O THR C 161 " pdb=" OG1 THR C 161 " model vdw 2.295 3.040 nonbonded pdb=" O SER F 79 " pdb=" N ASP F 82 " model vdw 2.345 3.120 ... (remaining 18830 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 71 or resid 73 through 85)) selection = (chain 'E' and (resid 71 or resid 73 through 85)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 0.150 2535 Z= 0.389 Angle : 0.923 11.812 3419 Z= 0.531 Chirality : 0.044 0.153 390 Planarity : 0.005 0.039 431 Dihedral : 17.631 166.335 941 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.28 % Allowed : 21.29 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.56 (0.46), residues: 307 helix: -0.70 (0.38), residues: 166 sheet: -0.37 (0.84), residues: 42 loop : -1.65 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 287 HIS 0.005 0.001 HIS C 222 PHE 0.015 0.001 PHE C 128 TYR 0.007 0.001 TYR A 72 ARG 0.003 0.000 ARG C 134 Details of bonding type rmsd hydrogen bonds : bond 0.18396 ( 119) hydrogen bonds : angle 7.70046 ( 343) covalent geometry : bond 0.00619 ( 2535) covalent geometry : angle 0.92339 ( 3419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: F 75 LEU cc_start: 0.9313 (mm) cc_final: 0.9106 (mp) REVERT: F 82 ASP cc_start: 0.9501 (m-30) cc_final: 0.9277 (m-30) REVERT: A 73 ARG cc_start: 0.9110 (tpt90) cc_final: 0.8073 (ttp-170) REVERT: C 47 GLU cc_start: 0.8001 (pp20) cc_final: 0.7759 (pp20) REVERT: C 73 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8136 (tmt170) REVERT: C 100 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 154 ASN cc_start: 0.8312 (t0) cc_final: 0.8109 (t0) REVERT: C 198 VAL cc_start: 0.8813 (m) cc_final: 0.8598 (p) REVERT: C 208 ASP cc_start: 0.7813 (p0) cc_final: 0.7602 (p0) outliers start: 6 outliers final: 2 residues processed: 122 average time/residue: 0.2035 time to fit residues: 27.6938 Evaluate side-chains 87 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 223 GLN C 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.098239 restraints weight = 33207.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103205 restraints weight = 8338.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106551 restraints weight = 4050.118| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2535 Z= 0.151 Angle : 0.718 6.220 3419 Z= 0.354 Chirality : 0.041 0.146 390 Planarity : 0.005 0.041 431 Dihedral : 12.152 147.071 367 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.56 % Allowed : 31.18 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.48), residues: 307 helix: 0.48 (0.40), residues: 166 sheet: -0.45 (0.80), residues: 46 loop : -1.48 (0.63), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.008 0.002 HIS C 222 PHE 0.021 0.002 PHE F 80 TYR 0.014 0.001 TYR F 72 ARG 0.009 0.001 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 119) hydrogen bonds : angle 5.23498 ( 343) covalent geometry : bond 0.00345 ( 2535) covalent geometry : angle 0.71829 ( 3419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8882 (tpt90) cc_final: 0.7975 (ttt180) REVERT: C 12 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8505 (pttt) REVERT: C 47 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8824 (pp20) REVERT: C 73 ARG cc_start: 0.8775 (mmm160) cc_final: 0.7748 (tmt170) REVERT: C 100 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 154 ASN cc_start: 0.8714 (t0) cc_final: 0.8406 (t0) REVERT: C 198 VAL cc_start: 0.9331 (m) cc_final: 0.9125 (p) REVERT: C 199 GLU cc_start: 0.8995 (pm20) cc_final: 0.8709 (pm20) REVERT: C 239 MET cc_start: 0.8366 (mtp) cc_final: 0.8121 (mtp) outliers start: 12 outliers final: 5 residues processed: 100 average time/residue: 0.1886 time to fit residues: 21.3971 Evaluate side-chains 94 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 161 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 GLN C 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.122489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097668 restraints weight = 33285.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102731 restraints weight = 8394.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106060 restraints weight = 4077.025| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2535 Z= 0.135 Angle : 0.739 9.823 3419 Z= 0.349 Chirality : 0.043 0.138 390 Planarity : 0.004 0.032 431 Dihedral : 11.030 127.393 365 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.70 % Allowed : 29.66 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.48), residues: 307 helix: 0.50 (0.40), residues: 166 sheet: -0.39 (0.81), residues: 46 loop : -1.33 (0.64), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 174 HIS 0.005 0.001 HIS C 222 PHE 0.013 0.002 PHE A 80 TYR 0.003 0.001 TYR C 202 ARG 0.006 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 119) hydrogen bonds : angle 4.88349 ( 343) covalent geometry : bond 0.00305 ( 2535) covalent geometry : angle 0.73858 ( 3419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8885 (tpt90) cc_final: 0.7948 (ttt180) REVERT: A 80 PHE cc_start: 0.9180 (t80) cc_final: 0.8913 (t80) REVERT: C 47 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8857 (pp20) REVERT: C 73 ARG cc_start: 0.8838 (mmm160) cc_final: 0.7708 (tmt170) REVERT: C 88 MET cc_start: 0.8250 (mmp) cc_final: 0.7980 (tpp) REVERT: C 100 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 154 ASN cc_start: 0.8718 (t0) cc_final: 0.8401 (t0) REVERT: C 198 VAL cc_start: 0.9361 (m) cc_final: 0.9147 (p) REVERT: C 199 GLU cc_start: 0.9012 (pm20) cc_final: 0.8767 (pm20) REVERT: C 219 LYS cc_start: 0.9211 (mmtp) cc_final: 0.9006 (mmtp) REVERT: C 239 MET cc_start: 0.8511 (mtp) cc_final: 0.8228 (mtp) outliers start: 15 outliers final: 5 residues processed: 98 average time/residue: 0.1938 time to fit residues: 21.4187 Evaluate side-chains 94 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain E residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.121670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097197 restraints weight = 32565.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102086 restraints weight = 8285.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105394 restraints weight = 4057.683| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2535 Z= 0.141 Angle : 0.728 7.697 3419 Z= 0.344 Chirality : 0.043 0.153 390 Planarity : 0.004 0.029 431 Dihedral : 10.477 107.331 365 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.08 % Allowed : 30.80 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.49), residues: 307 helix: 0.56 (0.40), residues: 166 sheet: -0.45 (0.81), residues: 46 loop : -1.22 (0.65), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.029 0.003 PHE C 80 TYR 0.002 0.001 TYR C 202 ARG 0.005 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 119) hydrogen bonds : angle 4.81946 ( 343) covalent geometry : bond 0.00323 ( 2535) covalent geometry : angle 0.72818 ( 3419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8923 (tpt90) cc_final: 0.7975 (ttp-170) REVERT: C 12 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8316 (mttt) REVERT: C 47 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8839 (pp20) REVERT: C 73 ARG cc_start: 0.8899 (mmm160) cc_final: 0.7721 (tmt170) REVERT: C 93 LYS cc_start: 0.8312 (mttt) cc_final: 0.7493 (pttt) REVERT: C 100 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8216 (tm-30) REVERT: C 154 ASN cc_start: 0.8749 (t0) cc_final: 0.8435 (t0) REVERT: C 198 VAL cc_start: 0.9382 (m) cc_final: 0.9165 (p) REVERT: C 199 GLU cc_start: 0.9006 (pm20) cc_final: 0.8785 (pm20) REVERT: C 239 MET cc_start: 0.8596 (mtp) cc_final: 0.8237 (mtp) REVERT: E 77 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.8895 (m110) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 0.1887 time to fit residues: 20.2753 Evaluate side-chains 96 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain E residue 77 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 GLN C 248 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097138 restraints weight = 38234.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102219 restraints weight = 8901.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105672 restraints weight = 4244.811| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2535 Z= 0.135 Angle : 0.758 9.859 3419 Z= 0.355 Chirality : 0.045 0.253 390 Planarity : 0.003 0.026 431 Dihedral : 10.193 99.170 365 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.08 % Allowed : 31.56 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.50), residues: 307 helix: 0.60 (0.41), residues: 166 sheet: -0.38 (0.81), residues: 51 loop : -1.20 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.013 0.002 PHE A 80 TYR 0.002 0.001 TYR A 72 ARG 0.004 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 119) hydrogen bonds : angle 4.85846 ( 343) covalent geometry : bond 0.00315 ( 2535) covalent geometry : angle 0.75846 ( 3419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8934 (tpt90) cc_final: 0.7976 (ttp-170) REVERT: C 12 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8342 (mttt) REVERT: C 47 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8836 (pp20) REVERT: C 73 ARG cc_start: 0.8902 (mmm160) cc_final: 0.7694 (tmt170) REVERT: C 93 LYS cc_start: 0.8271 (mttt) cc_final: 0.7485 (pttt) REVERT: C 100 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8252 (tm-30) REVERT: C 154 ASN cc_start: 0.8734 (t0) cc_final: 0.8416 (t0) REVERT: C 198 VAL cc_start: 0.9373 (m) cc_final: 0.9143 (p) REVERT: C 239 MET cc_start: 0.8646 (mtp) cc_final: 0.8220 (mtp) REVERT: E 77 ASN cc_start: 0.9288 (OUTLIER) cc_final: 0.8892 (m110) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 0.1789 time to fit residues: 19.3558 Evaluate side-chains 97 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 77 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 GLN C 248 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.121041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096226 restraints weight = 34221.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101216 restraints weight = 8377.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104559 restraints weight = 4065.153| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2535 Z= 0.154 Angle : 0.763 8.055 3419 Z= 0.362 Chirality : 0.044 0.208 390 Planarity : 0.003 0.024 431 Dihedral : 9.926 94.449 365 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.84 % Allowed : 31.18 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.50), residues: 307 helix: 0.71 (0.41), residues: 166 sheet: 0.03 (1.01), residues: 35 loop : -1.25 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.005 0.001 HIS C 222 PHE 0.015 0.002 PHE E 80 TYR 0.005 0.001 TYR C 202 ARG 0.004 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 119) hydrogen bonds : angle 4.84305 ( 343) covalent geometry : bond 0.00361 ( 2535) covalent geometry : angle 0.76286 ( 3419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8957 (tpt90) cc_final: 0.7965 (ttt180) REVERT: C 12 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8427 (mttt) REVERT: C 42 CYS cc_start: 0.9018 (m) cc_final: 0.8487 (t) REVERT: C 47 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8854 (pp20) REVERT: C 73 ARG cc_start: 0.8906 (mmm160) cc_final: 0.7653 (tmt170) REVERT: C 93 LYS cc_start: 0.8296 (mttt) cc_final: 0.7495 (pttt) REVERT: C 100 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8274 (tm-30) REVERT: C 154 ASN cc_start: 0.8763 (t0) cc_final: 0.8426 (t0) REVERT: C 239 MET cc_start: 0.8673 (mtp) cc_final: 0.8232 (mtp) REVERT: E 77 ASN cc_start: 0.9314 (OUTLIER) cc_final: 0.8884 (p0) outliers start: 18 outliers final: 12 residues processed: 95 average time/residue: 0.1968 time to fit residues: 21.3225 Evaluate side-chains 99 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 77 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.0270 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.097891 restraints weight = 28792.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.102733 restraints weight = 8084.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105991 restraints weight = 4035.670| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2535 Z= 0.139 Angle : 0.775 11.906 3419 Z= 0.362 Chirality : 0.043 0.158 390 Planarity : 0.003 0.025 431 Dihedral : 9.711 90.396 365 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.70 % Allowed : 31.18 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.50), residues: 307 helix: 0.75 (0.41), residues: 166 sheet: -0.03 (0.99), residues: 35 loop : -1.18 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.004 0.001 HIS C 222 PHE 0.013 0.002 PHE C 280 TYR 0.004 0.001 TYR C 202 ARG 0.003 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 119) hydrogen bonds : angle 4.76866 ( 343) covalent geometry : bond 0.00333 ( 2535) covalent geometry : angle 0.77466 ( 3419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8962 (tpt90) cc_final: 0.7974 (ttt180) REVERT: C 12 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8346 (mttt) REVERT: C 47 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8827 (pp20) REVERT: C 73 ARG cc_start: 0.8940 (mmm160) cc_final: 0.7666 (tmt170) REVERT: C 93 LYS cc_start: 0.8323 (mttt) cc_final: 0.7526 (pttt) REVERT: C 100 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8240 (tm-30) REVERT: C 154 ASN cc_start: 0.8741 (t0) cc_final: 0.8420 (t0) REVERT: C 239 MET cc_start: 0.8659 (mtp) cc_final: 0.8220 (mtp) REVERT: C 275 ARG cc_start: 0.5297 (mmt180) cc_final: 0.4056 (ttm170) REVERT: E 77 ASN cc_start: 0.9284 (m110) cc_final: 0.8931 (p0) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.1959 time to fit residues: 20.8058 Evaluate side-chains 92 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.0020 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.0040 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099997 restraints weight = 25161.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.104991 restraints weight = 7440.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108263 restraints weight = 3713.468| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2535 Z= 0.133 Angle : 0.790 11.916 3419 Z= 0.369 Chirality : 0.044 0.155 390 Planarity : 0.003 0.024 431 Dihedral : 9.551 84.863 365 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.80 % Allowed : 34.98 % Favored : 61.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.49), residues: 307 helix: 0.72 (0.41), residues: 166 sheet: -0.99 (0.89), residues: 35 loop : -1.08 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 174 HIS 0.010 0.002 HIS C 222 PHE 0.020 0.002 PHE A 80 TYR 0.016 0.001 TYR F 72 ARG 0.003 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 119) hydrogen bonds : angle 4.77785 ( 343) covalent geometry : bond 0.00322 ( 2535) covalent geometry : angle 0.78972 ( 3419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8928 (tpt90) cc_final: 0.8018 (ttt180) REVERT: C 12 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8486 (mttt) REVERT: C 47 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8810 (pp20) REVERT: C 73 ARG cc_start: 0.8930 (mmm160) cc_final: 0.7624 (tmt170) REVERT: C 93 LYS cc_start: 0.8234 (mttt) cc_final: 0.7447 (pttt) REVERT: C 100 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8243 (tm-30) REVERT: C 154 ASN cc_start: 0.8721 (t0) cc_final: 0.8409 (t0) REVERT: C 199 GLU cc_start: 0.8928 (pm20) cc_final: 0.8692 (pm20) REVERT: C 239 MET cc_start: 0.8618 (mtp) cc_final: 0.8161 (mtp) REVERT: C 275 ARG cc_start: 0.5323 (mmt180) cc_final: 0.4114 (ttm170) REVERT: E 77 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8852 (p0) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.1906 time to fit residues: 18.9470 Evaluate side-chains 92 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain E residue 77 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN E 77 ASN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.122560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.097214 restraints weight = 34173.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102391 restraints weight = 8512.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105846 restraints weight = 4096.878| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2535 Z= 0.157 Angle : 0.820 12.393 3419 Z= 0.388 Chirality : 0.046 0.215 390 Planarity : 0.003 0.024 431 Dihedral : 9.478 84.613 365 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.32 % Allowed : 34.22 % Favored : 60.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.49), residues: 307 helix: 0.44 (0.40), residues: 172 sheet: -1.07 (0.90), residues: 35 loop : -0.92 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.008 0.001 HIS C 222 PHE 0.024 0.002 PHE F 80 TYR 0.005 0.001 TYR C 106 ARG 0.003 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 119) hydrogen bonds : angle 4.77622 ( 343) covalent geometry : bond 0.00372 ( 2535) covalent geometry : angle 0.82025 ( 3419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8990 (tpt90) cc_final: 0.7978 (ttt180) REVERT: C 12 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8469 (mttt) REVERT: C 47 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8827 (pp20) REVERT: C 73 ARG cc_start: 0.8949 (mmm160) cc_final: 0.7639 (tmt170) REVERT: C 93 LYS cc_start: 0.8148 (mttt) cc_final: 0.7398 (pttt) REVERT: C 100 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8384 (tm-30) REVERT: C 154 ASN cc_start: 0.8754 (t0) cc_final: 0.8429 (t0) REVERT: C 199 GLU cc_start: 0.8937 (pm20) cc_final: 0.8712 (pm20) REVERT: C 239 MET cc_start: 0.8681 (mtp) cc_final: 0.8272 (mtp) REVERT: C 275 ARG cc_start: 0.5423 (mmt180) cc_final: 0.4021 (ttm170) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.1897 time to fit residues: 18.6895 Evaluate side-chains 92 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain E residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN C 248 ASN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.123306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.098080 restraints weight = 30869.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103201 restraints weight = 8126.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106556 restraints weight = 3946.414| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2535 Z= 0.138 Angle : 0.793 10.611 3419 Z= 0.371 Chirality : 0.044 0.158 390 Planarity : 0.003 0.024 431 Dihedral : 9.420 86.425 365 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.18 % Allowed : 34.98 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.49), residues: 307 helix: 0.45 (0.40), residues: 172 sheet: -1.07 (0.89), residues: 35 loop : -0.86 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.007 0.001 HIS C 222 PHE 0.021 0.002 PHE F 80 TYR 0.015 0.001 TYR F 72 ARG 0.003 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 119) hydrogen bonds : angle 4.67897 ( 343) covalent geometry : bond 0.00331 ( 2535) covalent geometry : angle 0.79295 ( 3419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8949 (tpt90) cc_final: 0.7907 (ttt180) REVERT: C 47 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8813 (pp20) REVERT: C 93 LYS cc_start: 0.8142 (mttt) cc_final: 0.7375 (pttt) REVERT: C 100 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8382 (tm-30) REVERT: C 154 ASN cc_start: 0.8689 (t0) cc_final: 0.8387 (t0) REVERT: C 199 GLU cc_start: 0.8918 (pm20) cc_final: 0.8706 (pm20) REVERT: C 239 MET cc_start: 0.8645 (mtp) cc_final: 0.8242 (mtp) REVERT: C 275 ARG cc_start: 0.5404 (mmt180) cc_final: 0.4025 (ttm170) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.1802 time to fit residues: 17.6821 Evaluate side-chains 87 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.0030 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN C 248 ASN E 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.125201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.101288 restraints weight = 20008.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106000 restraints weight = 6563.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109159 restraints weight = 3405.605| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2535 Z= 0.135 Angle : 0.816 11.102 3419 Z= 0.382 Chirality : 0.044 0.165 390 Planarity : 0.003 0.033 431 Dihedral : 9.339 88.286 365 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.42 % Allowed : 36.12 % Favored : 60.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.48), residues: 307 helix: 0.30 (0.40), residues: 172 sheet: -1.13 (0.88), residues: 35 loop : -0.83 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 174 HIS 0.006 0.001 HIS C 222 PHE 0.018 0.002 PHE F 80 TYR 0.006 0.001 TYR C 251 ARG 0.003 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 119) hydrogen bonds : angle 4.62938 ( 343) covalent geometry : bond 0.00320 ( 2535) covalent geometry : angle 0.81639 ( 3419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1443.40 seconds wall clock time: 25 minutes 56.23 seconds (1556.23 seconds total)