Starting phenix.real_space_refine on Thu Nov 14 00:01:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j28_35947/11_2024/8j28_35947.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j28_35947/11_2024/8j28_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j28_35947/11_2024/8j28_35947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j28_35947/11_2024/8j28_35947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j28_35947/11_2024/8j28_35947.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j28_35947/11_2024/8j28_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-5513/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: 3.38, per 1000 atoms: 1.35 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: 0.81 Conformation dependent library (CDL) restraints added in 606.6 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: 0.66 Time building geometry restraints manager: 0.84 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.950 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- 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= 0.359 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 *********************** 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 : 0.306 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: 0.2097 time to fit residues: 28.5581 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 : 0.296 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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= 0.219 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 *********************** 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 : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.9045 (tpt90) cc_final: 0.8091 (ttt180) REVERT: C 73 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8022 (tmt170) REVERT: C 100 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7716 (tm-30) REVERT: C 208 ASP cc_start: 0.7773 (p0) cc_final: 0.7539 (p0) outliers start: 12 outliers final: 5 residues processed: 100 average time/residue: 0.1903 time to fit residues: 21.5211 Evaluate side-chains 93 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL 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 14 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3844 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= 0.225 Angle : 0.744 9.764 3419 Z= 0.355 Chirality : 0.043 0.141 390 Planarity : 0.004 0.034 431 Dihedral : 11.048 124.728 365 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 7.22 % Allowed : 28.52 % 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: -0.40 (0.49), residues: 307 helix: 0.49 (0.40), residues: 166 sheet: -0.64 (0.80), residues: 48 loop : -1.24 (0.65), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 174 HIS 0.005 0.001 HIS C 222 PHE 0.013 0.002 PHE C 217 TYR 0.004 0.001 TYR C 202 ARG 0.006 0.001 ARG C 129 *********************** 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 109 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.9062 (tpt90) cc_final: 0.8082 (ttt180) REVERT: A 80 PHE cc_start: 0.9044 (t80) cc_final: 0.8772 (t80) REVERT: C 73 ARG cc_start: 0.8628 (mmm160) cc_final: 0.7866 (tmt170) REVERT: C 100 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 154 ASN cc_start: 0.7993 (t0) cc_final: 0.7787 (t0) REVERT: C 208 ASP cc_start: 0.7857 (p0) cc_final: 0.7602 (p0) outliers start: 19 outliers final: 8 residues processed: 100 average time/residue: 0.2040 time to fit residues: 22.9909 Evaluate side-chains 96 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 117 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU 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 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.0470 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2535 Z= 0.199 Angle : 0.740 7.731 3419 Z= 0.353 Chirality : 0.044 0.174 390 Planarity : 0.004 0.029 431 Dihedral : 10.544 108.315 365 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.32 % Allowed : 31.56 % 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: -0.30 (0.49), residues: 307 helix: 0.52 (0.40), residues: 166 sheet: -0.45 (0.82), residues: 46 loop : -1.19 (0.65), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.029 0.003 PHE C 80 TYR 0.003 0.001 TYR C 202 ARG 0.005 0.000 ARG C 129 *********************** 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 101 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.9063 (tpt90) cc_final: 0.8093 (ttp-170) REVERT: C 73 ARG cc_start: 0.8656 (mmm160) cc_final: 0.7823 (tmt170) REVERT: C 93 LYS cc_start: 0.8065 (mttt) cc_final: 0.7796 (pttt) REVERT: C 100 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 154 ASN cc_start: 0.8063 (t0) cc_final: 0.7838 (t0) REVERT: C 208 ASP cc_start: 0.7879 (p0) cc_final: 0.7616 (p0) REVERT: E 77 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8555 (m110) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.1855 time to fit residues: 20.2343 Evaluate side-chains 95 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 48 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 70 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2535 Z= 0.292 Angle : 0.792 9.658 3419 Z= 0.377 Chirality : 0.047 0.272 390 Planarity : 0.003 0.025 431 Dihedral : 10.422 100.599 365 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 7.22 % Allowed : 30.42 % 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: -0.27 (0.49), residues: 307 helix: 0.55 (0.41), residues: 166 sheet: 0.16 (1.04), residues: 30 loop : -1.32 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.013 0.002 PHE F 80 TYR 0.003 0.001 TYR C 107 ARG 0.004 0.001 ARG C 8 *********************** 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 107 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.9106 (tpt90) cc_final: 0.8106 (ttt180) REVERT: C 73 ARG cc_start: 0.8679 (mmm160) cc_final: 0.7794 (tmt170) REVERT: C 100 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7863 (tm-30) REVERT: C 154 ASN cc_start: 0.8144 (t0) cc_final: 0.7924 (t0) REVERT: C 208 ASP cc_start: 0.8098 (p0) cc_final: 0.7751 (p0) REVERT: C 275 ARG cc_start: 0.5302 (mmt180) cc_final: 0.4656 (ttm170) REVERT: E 77 ASN cc_start: 0.8876 (m110) cc_final: 0.8519 (m110) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.1839 time to fit residues: 20.7703 Evaluate side-chains 98 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain E residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4607 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= 0.205 Angle : 0.761 9.291 3419 Z= 0.356 Chirality : 0.044 0.195 390 Planarity : 0.003 0.028 431 Dihedral : 10.160 88.605 365 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 7.60 % Allowed : 29.28 % 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: -0.21 (0.48), residues: 307 helix: 0.60 (0.40), residues: 166 sheet: 0.01 (1.02), residues: 30 loop : -1.22 (0.59), residues: 111 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 0.012 0.002 PHE A 80 TYR 0.003 0.001 TYR C 202 ARG 0.004 0.000 ARG C 129 *********************** 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 104 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.9091 (tpt90) cc_final: 0.8089 (ttt180) REVERT: C 73 ARG cc_start: 0.8653 (mmm160) cc_final: 0.7732 (tmt170) REVERT: C 100 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7754 (tm-30) REVERT: C 154 ASN cc_start: 0.8112 (t0) cc_final: 0.7860 (t0) REVERT: C 208 ASP cc_start: 0.8060 (p0) cc_final: 0.7706 (p0) REVERT: C 275 ARG cc_start: 0.5292 (mmt180) cc_final: 0.4586 (ttm170) outliers start: 20 outliers final: 13 residues processed: 96 average time/residue: 0.1888 time to fit residues: 20.7357 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 : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 23 THR 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 109 THR 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 198 VAL Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 25 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4828 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= 0.195 Angle : 0.776 8.048 3419 Z= 0.360 Chirality : 0.044 0.157 390 Planarity : 0.003 0.034 431 Dihedral : 10.025 92.075 365 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.56 % Allowed : 32.70 % Favored : 62.74 % 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: -0.24 (0.48), residues: 307 helix: 0.65 (0.40), residues: 166 sheet: -0.86 (0.91), residues: 35 loop : -1.08 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.020 0.002 PHE F 80 TYR 0.005 0.001 TYR C 202 ARG 0.004 0.000 ARG C 129 *********************** 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 100 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.9065 (tpt90) cc_final: 0.8086 (ttt180) REVERT: C 17 ILE cc_start: 0.8815 (mt) cc_final: 0.8488 (tt) REVERT: C 100 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 154 ASN cc_start: 0.8084 (t0) cc_final: 0.7822 (t0) REVERT: C 208 ASP cc_start: 0.8084 (p0) cc_final: 0.7702 (p0) REVERT: C 275 ARG cc_start: 0.5136 (mmt180) cc_final: 0.4388 (ttm170) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.1762 time to fit residues: 19.0314 Evaluate side-chains 95 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 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 109 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 159 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN C 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2535 Z= 0.204 Angle : 0.806 8.268 3419 Z= 0.372 Chirality : 0.043 0.153 390 Planarity : 0.003 0.029 431 Dihedral : 9.992 98.571 365 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.18 % Allowed : 32.70 % 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: -0.25 (0.48), residues: 307 helix: 0.68 (0.41), residues: 166 sheet: -0.95 (0.89), residues: 35 loop : -1.12 (0.60), residues: 106 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 0.019 0.002 PHE F 80 TYR 0.008 0.001 TYR C 106 ARG 0.003 0.000 ARG C 129 *********************** 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 102 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.9046 (tpt90) cc_final: 0.8097 (ttt180) REVERT: C 17 ILE cc_start: 0.8837 (mt) cc_final: 0.8545 (tt) REVERT: C 100 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 154 ASN cc_start: 0.8088 (t0) cc_final: 0.7825 (t0) REVERT: C 275 ARG cc_start: 0.5182 (mmt180) cc_final: 0.4385 (ttm170) outliers start: 11 outliers final: 10 residues processed: 95 average time/residue: 0.1777 time to fit residues: 19.4462 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 : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 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 109 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 23 optimal weight: 10.0000 chunk 2 optimal weight: 0.0030 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.1832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN E 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2535 Z= 0.229 Angle : 0.817 8.673 3419 Z= 0.386 Chirality : 0.046 0.159 390 Planarity : 0.003 0.028 431 Dihedral : 9.835 104.627 365 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.56 % Allowed : 33.08 % 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: -0.22 (0.49), residues: 307 helix: 0.66 (0.41), residues: 166 sheet: -0.89 (0.91), residues: 35 loop : -1.05 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.019 0.002 PHE F 80 TYR 0.006 0.001 TYR C 106 ARG 0.003 0.000 ARG C 129 *********************** 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 99 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.285 Fit side-chains REVERT: A 73 ARG cc_start: 0.9085 (tpt90) cc_final: 0.8098 (ttt180) REVERT: C 100 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7910 (tm-30) REVERT: C 154 ASN cc_start: 0.8114 (t0) cc_final: 0.7823 (t0) REVERT: C 275 ARG cc_start: 0.5342 (mmt180) cc_final: 0.5133 (ttm-80) outliers start: 12 outliers final: 11 residues processed: 93 average time/residue: 0.1761 time to fit residues: 18.7276 Evaluate side-chains 97 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 23 THR 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 109 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.0040 chunk 4 optimal weight: 0.0060 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.3608 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2535 Z= 0.197 Angle : 0.845 9.422 3419 Z= 0.398 Chirality : 0.044 0.143 390 Planarity : 0.003 0.029 431 Dihedral : 9.711 109.916 365 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.56 % Allowed : 33.08 % 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: -0.37 (0.48), residues: 307 helix: 0.42 (0.40), residues: 173 sheet: -0.99 (0.90), residues: 35 loop : -0.95 (0.62), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.020 0.002 PHE F 80 TYR 0.014 0.001 TYR C 202 ARG 0.003 0.000 ARG C 129 ********************** 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 96 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.302 Fit side-chains REVERT: A 73 ARG cc_start: 0.9050 (tpt90) cc_final: 0.8062 (ttt180) REVERT: C 100 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 154 ASN cc_start: 0.8083 (t0) cc_final: 0.7808 (t0) REVERT: C 199 GLU cc_start: 0.7746 (pm20) cc_final: 0.7235 (pm20) REVERT: C 202 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: C 275 ARG cc_start: 0.5251 (mmt180) cc_final: 0.4603 (ttm170) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.1952 time to fit residues: 19.6814 Evaluate side-chains 90 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 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 109 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 202 TYR Chi-restraints excluded: chain C residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.124470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101976 restraints weight = 17358.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.106468 restraints weight = 6208.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.109372 restraints weight = 3359.199| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2535 Z= 0.266 Angle : 0.886 11.985 3419 Z= 0.435 Chirality : 0.045 0.169 390 Planarity : 0.004 0.028 431 Dihedral : 9.376 115.993 363 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.94 % Allowed : 33.84 % 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: -0.35 (0.49), residues: 307 helix: 0.46 (0.41), residues: 173 sheet: -1.00 (0.91), residues: 35 loop : -1.01 (0.63), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 174 HIS 0.003 0.001 HIS C 222 PHE 0.019 0.002 PHE F 80 TYR 0.009 0.001 TYR C 202 ARG 0.003 0.001 ARG A 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1118.95 seconds wall clock time: 21 minutes 0.14 seconds (1260.14 seconds total)