Starting phenix.real_space_refine on Fri Aug 22 14:21:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3r_42951/08_2025/8v3r_42951.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3r_42951/08_2025/8v3r_42951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v3r_42951/08_2025/8v3r_42951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3r_42951/08_2025/8v3r_42951.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3r_42951/08_2025/8v3r_42951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3r_42951/08_2025/8v3r_42951.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Zn 1 6.06 5 S 23 5.16 5 C 2521 2.51 5 N 711 2.21 5 O 697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3953 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3914 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 35, 'TRANS': 465} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 109 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 1.24, per 1000 atoms: 0.31 Number of scatterers: 3953 At special positions: 0 Unit cell: (80.925, 77.19, 72.21, 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) Zn 1 29.99 S 23 16.00 O 697 8.00 N 711 7.00 C 2521 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 159.4 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 252 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 434 " 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 4 sheets defined 31.4% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 256 through 270 removed outlier: 3.910A pdb=" N PHE A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 323 through 340 Processing helix chain 'A' and resid 451 through 467 removed outlier: 4.340A pdb=" N TYR A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Proline residue: A 462 - end of helix Processing helix chain 'A' and resid 481 through 486 removed outlier: 3.890A pdb=" N TYR A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 removed outlier: 3.668A pdb=" N GLY A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 551 through 570 removed outlier: 3.505A pdb=" N MET A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 585 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 6.747A pdb=" N VAL A 110 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG A 118 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 24 removed outlier: 6.471A pdb=" N TYR A 52 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN A 91 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 54 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 198 removed outlier: 7.159A pdb=" N VAL A 205 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 245 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE A 289 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 247 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR A 429 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 220 removed outlier: 5.426A pdb=" N ARG A 238 " --> pdb=" O ARG A 217 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 432 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: 0.60 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 724 1.31 - 1.44: 1095 1.44 - 1.57: 2207 1.57 - 1.69: 4 1.69 - 1.82: 35 Bond restraints: 4065 Sorted by residual: bond pdb=" CD2 HIS A 436 " pdb=" NE2 HIS A 436 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" CZ ARG A 303 " pdb=" NH2 ARG A 303 " ideal model delta sigma weight residual 1.330 1.280 0.050 1.30e-02 5.92e+03 1.50e+01 bond pdb=" CZ ARG A 303 " pdb=" NH1 ARG A 303 " ideal model delta sigma weight residual 1.323 1.274 0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" CZ ARG A 220 " pdb=" NH2 ARG A 220 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" CZ ARG A 299 " pdb=" NH2 ARG A 299 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.00e+01 ... (remaining 4060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 3726 1.44 - 2.89: 1402 2.89 - 4.33: 321 4.33 - 5.78: 60 5.78 - 7.22: 12 Bond angle restraints: 5521 Sorted by residual: angle pdb=" N PRO A 542 " pdb=" CA PRO A 542 " pdb=" CB PRO A 542 " ideal model delta sigma weight residual 103.19 106.12 -2.93 5.60e-01 3.19e+00 2.75e+01 angle pdb=" OD1 ASN A 518 " pdb=" CG ASN A 518 " pdb=" ND2 ASN A 518 " ideal model delta sigma weight residual 122.60 117.43 5.17 1.00e+00 1.00e+00 2.67e+01 angle pdb=" OE1 GLN A 134 " pdb=" CD GLN A 134 " pdb=" NE2 GLN A 134 " ideal model delta sigma weight residual 122.60 117.72 4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" CA ASN A 478 " pdb=" CB ASN A 478 " pdb=" CG ASN A 478 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" CB HIS A 434 " pdb=" CG HIS A 434 " pdb=" CD2 HIS A 434 " ideal model delta sigma weight residual 131.20 125.36 5.84 1.30e+00 5.92e-01 2.02e+01 ... (remaining 5516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 2240 17.77 - 35.54: 130 35.54 - 53.31: 25 53.31 - 71.07: 6 71.07 - 88.84: 3 Dihedral angle restraints: 2404 sinusoidal: 930 harmonic: 1474 Sorted by residual: dihedral pdb=" CA THR A 112 " pdb=" C THR A 112 " pdb=" N LEU A 113 " pdb=" CA LEU A 113 " ideal model delta harmonic sigma weight residual 180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TYR A 429 " pdb=" C TYR A 429 " pdb=" N TYR A 430 " pdb=" CA TYR A 430 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA HIS A 583 " pdb=" C HIS A 583 " pdb=" N SER A 584 " pdb=" CA SER A 584 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 2401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 376 0.073 - 0.147: 158 0.147 - 0.220: 49 0.220 - 0.293: 5 0.293 - 0.367: 1 Chirality restraints: 589 Sorted by residual: chirality pdb=" CA SER A 16 " pdb=" N SER A 16 " pdb=" C SER A 16 " pdb=" CB SER A 16 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA GLU M1001 " pdb=" N GLU M1001 " pdb=" C GLU M1001 " pdb=" CB GLU M1001 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA ASN A 293 " pdb=" N ASN A 293 " pdb=" C ASN A 293 " pdb=" CB ASN A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 586 not shown) Planarity restraints: 723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 192 " -0.063 2.00e-02 2.50e+03 4.72e-02 3.34e+01 pdb=" CG HIS A 192 " 0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS A 192 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS A 192 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A 192 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS A 192 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 575 " 0.055 2.00e-02 2.50e+03 3.32e-02 2.76e+01 pdb=" CG TRP A 575 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP A 575 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP A 575 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP A 575 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 575 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 575 " -0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 575 " 0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 575 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP A 575 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 335 " -0.067 2.00e-02 2.50e+03 3.59e-02 2.58e+01 pdb=" CG TYR A 335 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 335 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 335 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 335 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 335 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 335 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 335 " -0.052 2.00e-02 2.50e+03 ... (remaining 720 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 2 2.34 - 2.98: 1834 2.98 - 3.62: 5806 3.62 - 4.26: 9266 4.26 - 4.90: 15535 Nonbonded interactions: 32443 Sorted by model distance: nonbonded pdb=" OE2 GLU A 255 " pdb="ZN ZN A 701 " model vdw 1.701 2.230 nonbonded pdb=" NH2 ARG A 500 " pdb=" OE1 GLU M1001 " model vdw 2.236 3.120 nonbonded pdb=" ND2 ASN A 312 " pdb=" O GLU M1001 " model vdw 2.366 3.120 nonbonded pdb=" CD GLU A 255 " pdb="ZN ZN A 701 " model vdw 2.375 2.460 nonbonded pdb=" OE1 GLU A 255 " pdb="ZN ZN A 701 " model vdw 2.473 2.230 ... (remaining 32438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.280 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.013 0.222 4068 Z= 0.759 Angle : 1.582 7.220 5521 Z= 1.060 Chirality : 0.086 0.367 589 Planarity : 0.012 0.081 723 Dihedral : 12.459 88.842 1452 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.24 % Allowed : 5.10 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.36), residues: 493 helix: 0.21 (0.39), residues: 142 sheet: 0.20 (0.55), residues: 85 loop : -0.72 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 220 TYR 0.067 0.014 TYR A 335 PHE 0.047 0.009 PHE A 265 TRP 0.055 0.016 TRP A 575 HIS 0.016 0.004 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.01202 ( 4065) covalent geometry : angle 1.58181 ( 5521) hydrogen bonds : bond 0.19579 ( 154) hydrogen bonds : angle 8.13867 ( 432) metal coordination : bond 0.21498 ( 2) Misc. bond : bond 0.04500 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 65 THR cc_start: 0.7815 (m) cc_final: 0.7499 (p) REVERT: A 68 GLU cc_start: 0.8535 (tt0) cc_final: 0.7961 (tt0) REVERT: A 93 MET cc_start: 0.7871 (mmm) cc_final: 0.7337 (mmm) REVERT: A 170 GLN cc_start: 0.6808 (mt0) cc_final: 0.6393 (mt0) REVERT: A 173 GLN cc_start: 0.7202 (mm110) cc_final: 0.6452 (pt0) REVERT: A 204 ARG cc_start: 0.8389 (mtp-110) cc_final: 0.8062 (mtp-110) REVERT: A 206 ASP cc_start: 0.7226 (t0) cc_final: 0.6844 (p0) REVERT: A 314 GLN cc_start: 0.8551 (mm110) cc_final: 0.8173 (mm110) REVERT: A 316 LEU cc_start: 0.9105 (mt) cc_final: 0.8498 (mt) REVERT: A 322 LEU cc_start: 0.8684 (mp) cc_final: 0.8340 (mt) REVERT: A 440 ARG cc_start: 0.7842 (mtm110) cc_final: 0.6581 (mtp180) REVERT: A 483 ASN cc_start: 0.7222 (t0) cc_final: 0.6605 (t0) REVERT: A 523 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7206 (ttm-80) REVERT: A 534 ASP cc_start: 0.8472 (p0) cc_final: 0.7935 (p0) REVERT: A 562 MET cc_start: 0.7820 (mtp) cc_final: 0.7578 (mtm) REVERT: A 598 ARG cc_start: 0.6705 (mmm160) cc_final: 0.6100 (mtm180) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.1012 time to fit residues: 11.5481 Evaluate side-chains 63 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.0870 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.0870 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.0030 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 overall best weight: 0.1346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115694 restraints weight = 5655.640| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.26 r_work: 0.3235 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4068 Z= 0.134 Angle : 0.596 10.085 5521 Z= 0.308 Chirality : 0.042 0.132 589 Planarity : 0.005 0.046 723 Dihedral : 5.532 56.269 563 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.43 % Allowed : 10.68 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.37), residues: 493 helix: 1.29 (0.41), residues: 143 sheet: 0.46 (0.52), residues: 93 loop : -0.38 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 590 TYR 0.013 0.002 TYR A 335 PHE 0.016 0.002 PHE A 153 TRP 0.003 0.001 TRP A 57 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4065) covalent geometry : angle 0.59569 ( 5521) hydrogen bonds : bond 0.04355 ( 154) hydrogen bonds : angle 5.71907 ( 432) metal coordination : bond 0.00579 ( 2) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7664 (mm110) cc_final: 0.7103 (pt0) REVERT: A 267 ASP cc_start: 0.7158 (m-30) cc_final: 0.6958 (m-30) REVERT: A 316 LEU cc_start: 0.9184 (mt) cc_final: 0.8669 (mt) REVERT: A 483 ASN cc_start: 0.7501 (t0) cc_final: 0.7142 (t0) REVERT: A 598 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7008 (mtm180) outliers start: 10 outliers final: 6 residues processed: 71 average time/residue: 0.0872 time to fit residues: 7.5827 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 24 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 14 optimal weight: 0.1980 overall best weight: 0.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 323 HIS A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113116 restraints weight = 5663.703| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.25 r_work: 0.3200 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4068 Z= 0.133 Angle : 0.557 9.039 5521 Z= 0.283 Chirality : 0.041 0.139 589 Planarity : 0.005 0.039 723 Dihedral : 5.316 55.691 563 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.91 % Allowed : 11.17 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.38), residues: 493 helix: 1.46 (0.42), residues: 144 sheet: 0.55 (0.53), residues: 93 loop : -0.37 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 590 TYR 0.012 0.002 TYR A 519 PHE 0.018 0.002 PHE A 546 TRP 0.004 0.001 TRP A 119 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4065) covalent geometry : angle 0.55660 ( 5521) hydrogen bonds : bond 0.03903 ( 154) hydrogen bonds : angle 5.29426 ( 432) metal coordination : bond 0.00108 ( 2) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7585 (mm110) cc_final: 0.7098 (pt0) REVERT: A 267 ASP cc_start: 0.7220 (m-30) cc_final: 0.6997 (m-30) REVERT: A 316 LEU cc_start: 0.9197 (mt) cc_final: 0.8644 (mt) REVERT: A 459 MET cc_start: 0.8421 (ttm) cc_final: 0.8149 (ttp) REVERT: A 483 ASN cc_start: 0.7522 (t0) cc_final: 0.7163 (t0) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.0848 time to fit residues: 6.4615 Evaluate side-chains 57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 48 optimal weight: 0.0970 chunk 4 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 49 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 overall best weight: 0.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.110377 restraints weight = 5652.208| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.25 r_work: 0.3164 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4068 Z= 0.140 Angle : 0.548 7.990 5521 Z= 0.279 Chirality : 0.042 0.156 589 Planarity : 0.004 0.032 723 Dihedral : 5.229 56.157 563 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.91 % Allowed : 10.68 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.38), residues: 493 helix: 1.43 (0.42), residues: 144 sheet: 0.79 (0.55), residues: 93 loop : -0.33 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 523 TYR 0.013 0.002 TYR A 519 PHE 0.014 0.002 PHE A 546 TRP 0.005 0.001 TRP A 575 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4065) covalent geometry : angle 0.54829 ( 5521) hydrogen bonds : bond 0.03645 ( 154) hydrogen bonds : angle 5.01548 ( 432) metal coordination : bond 0.00293 ( 2) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7610 (mm110) cc_final: 0.7247 (pt0) REVERT: A 316 LEU cc_start: 0.9215 (mt) cc_final: 0.8596 (mt) REVERT: A 464 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8907 (mt) REVERT: A 483 ASN cc_start: 0.7415 (t0) cc_final: 0.7134 (t0) REVERT: A 519 TYR cc_start: 0.8685 (m-80) cc_final: 0.7976 (m-80) REVERT: A 598 ARG cc_start: 0.7576 (mmm160) cc_final: 0.7002 (mtm180) outliers start: 12 outliers final: 9 residues processed: 60 average time/residue: 0.0745 time to fit residues: 5.6109 Evaluate side-chains 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.0670 chunk 24 optimal weight: 0.0870 chunk 42 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 overall best weight: 0.1896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109516 restraints weight = 5707.964| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.25 r_work: 0.3128 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4068 Z= 0.148 Angle : 0.544 7.955 5521 Z= 0.275 Chirality : 0.041 0.149 589 Planarity : 0.004 0.029 723 Dihedral : 5.171 55.920 563 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.43 % Allowed : 13.83 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.38), residues: 493 helix: 1.45 (0.42), residues: 144 sheet: 0.78 (0.55), residues: 93 loop : -0.34 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 523 TYR 0.013 0.002 TYR A 519 PHE 0.012 0.002 PHE A 245 TRP 0.004 0.001 TRP A 119 HIS 0.002 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4065) covalent geometry : angle 0.54368 ( 5521) hydrogen bonds : bond 0.03616 ( 154) hydrogen bonds : angle 5.01618 ( 432) metal coordination : bond 0.00313 ( 2) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7585 (mm110) cc_final: 0.7309 (pt0) REVERT: A 206 ASP cc_start: 0.7868 (m-30) cc_final: 0.7648 (m-30) REVERT: A 316 LEU cc_start: 0.9208 (mt) cc_final: 0.9005 (mt) REVERT: A 440 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7593 (mtp180) REVERT: A 464 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8958 (mt) REVERT: A 483 ASN cc_start: 0.7407 (t0) cc_final: 0.7140 (t0) REVERT: A 519 TYR cc_start: 0.8616 (m-80) cc_final: 0.7854 (m-80) REVERT: A 598 ARG cc_start: 0.7605 (mmm160) cc_final: 0.7070 (mtm180) outliers start: 10 outliers final: 8 residues processed: 58 average time/residue: 0.0863 time to fit residues: 6.0610 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.2980 chunk 30 optimal weight: 0.0970 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 chunk 13 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.0070 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110166 restraints weight = 5766.134| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.25 r_work: 0.3150 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4068 Z= 0.120 Angle : 0.520 7.898 5521 Z= 0.261 Chirality : 0.040 0.149 589 Planarity : 0.004 0.028 723 Dihedral : 4.969 52.524 563 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.91 % Allowed : 13.11 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.38), residues: 493 helix: 1.35 (0.42), residues: 146 sheet: 0.69 (0.54), residues: 100 loop : -0.42 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 590 TYR 0.011 0.001 TYR A 519 PHE 0.011 0.001 PHE A 153 TRP 0.004 0.001 TRP A 592 HIS 0.002 0.000 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4065) covalent geometry : angle 0.52008 ( 5521) hydrogen bonds : bond 0.03295 ( 154) hydrogen bonds : angle 4.89906 ( 432) metal coordination : bond 0.00231 ( 2) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7883 (m-30) cc_final: 0.7667 (m-30) REVERT: A 226 GLN cc_start: 0.7761 (mt0) cc_final: 0.7427 (mt0) REVERT: A 316 LEU cc_start: 0.9242 (mt) cc_final: 0.9036 (mt) REVERT: A 440 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7471 (mtp180) REVERT: A 464 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8944 (mt) REVERT: A 483 ASN cc_start: 0.7378 (t0) cc_final: 0.7144 (t0) REVERT: A 519 TYR cc_start: 0.8657 (m-80) cc_final: 0.7903 (m-80) REVERT: A 556 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: A 598 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7175 (mtm180) outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.0857 time to fit residues: 6.1306 Evaluate side-chains 57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.0070 chunk 27 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 0.0070 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.0050 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 overall best weight: 0.0408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111527 restraints weight = 5801.456| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.33 r_work: 0.3184 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4068 Z= 0.094 Angle : 0.506 7.925 5521 Z= 0.252 Chirality : 0.040 0.144 589 Planarity : 0.004 0.030 723 Dihedral : 4.739 46.565 563 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.18 % Allowed : 15.29 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.38), residues: 493 helix: 1.47 (0.42), residues: 146 sheet: 0.66 (0.53), residues: 100 loop : -0.44 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 598 TYR 0.009 0.001 TYR A 157 PHE 0.012 0.001 PHE A 546 TRP 0.006 0.001 TRP A 592 HIS 0.004 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4065) covalent geometry : angle 0.50552 ( 5521) hydrogen bonds : bond 0.03033 ( 154) hydrogen bonds : angle 4.88363 ( 432) metal coordination : bond 0.00067 ( 2) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7903 (m-30) cc_final: 0.7679 (m-30) REVERT: A 316 LEU cc_start: 0.9223 (mt) cc_final: 0.9014 (mt) REVERT: A 440 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7199 (mtp180) REVERT: A 464 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8945 (mt) REVERT: A 483 ASN cc_start: 0.7330 (t0) cc_final: 0.7040 (t0) REVERT: A 519 TYR cc_start: 0.8616 (m-80) cc_final: 0.7741 (m-80) REVERT: A 556 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: A 598 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7037 (mtm180) outliers start: 9 outliers final: 5 residues processed: 58 average time/residue: 0.0971 time to fit residues: 6.7271 Evaluate side-chains 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.2980 chunk 42 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 27 optimal weight: 0.0770 chunk 2 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.0010 chunk 46 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 overall best weight: 0.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110785 restraints weight = 5783.918| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.30 r_work: 0.3165 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4068 Z= 0.119 Angle : 0.520 8.133 5521 Z= 0.259 Chirality : 0.040 0.143 589 Planarity : 0.004 0.052 723 Dihedral : 4.673 43.441 563 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.18 % Allowed : 15.29 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.38), residues: 493 helix: 1.35 (0.42), residues: 146 sheet: 0.65 (0.53), residues: 100 loop : -0.43 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 590 TYR 0.010 0.001 TYR A 519 PHE 0.011 0.001 PHE A 265 TRP 0.003 0.001 TRP A 119 HIS 0.002 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4065) covalent geometry : angle 0.52042 ( 5521) hydrogen bonds : bond 0.03175 ( 154) hydrogen bonds : angle 4.88134 ( 432) metal coordination : bond 0.00224 ( 2) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 179 HIS cc_start: 0.6289 (p-80) cc_final: 0.6044 (p90) REVERT: A 440 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7189 (mtp180) REVERT: A 464 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8965 (mt) REVERT: A 483 ASN cc_start: 0.7314 (t0) cc_final: 0.7058 (t0) REVERT: A 519 TYR cc_start: 0.8643 (m-80) cc_final: 0.7758 (m-80) REVERT: A 556 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: A 593 MET cc_start: 0.9191 (tpp) cc_final: 0.8395 (tpp) REVERT: A 598 ARG cc_start: 0.7625 (mmm160) cc_final: 0.7001 (mtm180) outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.0833 time to fit residues: 5.8661 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.0970 chunk 42 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 41 optimal weight: 0.3980 chunk 8 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106160 restraints weight = 5826.091| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.26 r_work: 0.3103 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 4068 Z= 0.194 Angle : 0.594 8.766 5521 Z= 0.299 Chirality : 0.043 0.165 589 Planarity : 0.005 0.043 723 Dihedral : 4.928 41.419 563 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.91 % Allowed : 14.32 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.39), residues: 493 helix: 1.12 (0.42), residues: 146 sheet: 0.87 (0.55), residues: 100 loop : -0.50 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 590 TYR 0.016 0.002 TYR A 519 PHE 0.015 0.002 PHE A 245 TRP 0.005 0.001 TRP A 592 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 4065) covalent geometry : angle 0.59431 ( 5521) hydrogen bonds : bond 0.03768 ( 154) hydrogen bonds : angle 4.95840 ( 432) metal coordination : bond 0.00481 ( 2) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 179 HIS cc_start: 0.6414 (p-80) cc_final: 0.6155 (p90) REVERT: A 440 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7508 (mtp180) REVERT: A 464 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8963 (mt) REVERT: A 483 ASN cc_start: 0.7408 (t0) cc_final: 0.7103 (t0) REVERT: A 519 TYR cc_start: 0.8750 (m-80) cc_final: 0.8103 (m-80) REVERT: A 556 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: A 593 MET cc_start: 0.9138 (tpp) cc_final: 0.8324 (tpp) REVERT: A 598 ARG cc_start: 0.7713 (mmm160) cc_final: 0.7231 (mtm180) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.0777 time to fit residues: 5.5792 Evaluate side-chains 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 4 optimal weight: 0.0010 chunk 24 optimal weight: 0.0770 chunk 22 optimal weight: 0.1980 chunk 23 optimal weight: 0.0980 chunk 25 optimal weight: 0.0670 chunk 43 optimal weight: 0.3980 chunk 13 optimal weight: 0.2980 chunk 8 optimal weight: 0.0870 overall best weight: 0.0638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109551 restraints weight = 5792.354| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.27 r_work: 0.3150 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4068 Z= 0.104 Angle : 0.539 8.386 5521 Z= 0.270 Chirality : 0.040 0.156 589 Planarity : 0.005 0.051 723 Dihedral : 4.599 31.542 563 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.43 % Allowed : 14.56 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.39), residues: 493 helix: 1.33 (0.43), residues: 144 sheet: 0.89 (0.55), residues: 100 loop : -0.39 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 590 TYR 0.009 0.001 TYR A 519 PHE 0.031 0.002 PHE A 546 TRP 0.003 0.000 TRP A 592 HIS 0.003 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4065) covalent geometry : angle 0.53910 ( 5521) hydrogen bonds : bond 0.03214 ( 154) hydrogen bonds : angle 4.93333 ( 432) metal coordination : bond 0.00103 ( 2) Misc. bond : bond 0.00019 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 440 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7194 (mtp180) REVERT: A 464 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8972 (mt) REVERT: A 483 ASN cc_start: 0.7355 (t0) cc_final: 0.7052 (t0) REVERT: A 519 TYR cc_start: 0.8639 (m-80) cc_final: 0.7741 (m-80) REVERT: A 546 PHE cc_start: 0.6540 (p90) cc_final: 0.5433 (m-80) REVERT: A 556 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: A 593 MET cc_start: 0.9139 (tpp) cc_final: 0.8499 (tpp) REVERT: A 598 ARG cc_start: 0.7591 (mmm160) cc_final: 0.7007 (mtm180) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.0870 time to fit residues: 6.2389 Evaluate side-chains 57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.0270 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.0770 chunk 37 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 2 optimal weight: 0.3980 chunk 34 optimal weight: 0.0970 chunk 14 optimal weight: 0.0870 overall best weight: 0.0710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.110473 restraints weight = 5796.720| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.28 r_work: 0.3164 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4068 Z= 0.105 Angle : 0.543 8.187 5521 Z= 0.271 Chirality : 0.040 0.149 589 Planarity : 0.005 0.054 723 Dihedral : 4.489 27.443 563 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.70 % Allowed : 16.02 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.39), residues: 493 helix: 1.41 (0.43), residues: 144 sheet: 0.85 (0.54), residues: 100 loop : -0.39 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 590 TYR 0.009 0.001 TYR A 519 PHE 0.032 0.002 PHE A 546 TRP 0.004 0.001 TRP A 592 HIS 0.002 0.000 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4065) covalent geometry : angle 0.54275 ( 5521) hydrogen bonds : bond 0.03149 ( 154) hydrogen bonds : angle 4.90570 ( 432) metal coordination : bond 0.00113 ( 2) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.54 seconds wall clock time: 22 minutes 44.77 seconds (1364.77 seconds total)