Starting phenix.real_space_refine on Sun Apr 27 01:08:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3r_42951/04_2025/8v3r_42951.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3r_42951/04_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_42951/04_2025/8v3r_42951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3r_42951/04_2025/8v3r_42951.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3r_42951/04_2025/8v3r_42951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3r_42951/04_2025/8v3r_42951.cif" } resolution = 3.4 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 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 2, 'GLU:plan': 14, 'ARG:plan': 6, 'ASP:plan': 5} 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: {'GLU:plan': 1, 'UNK:plan-1': 4} 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: 4.82, per 1000 atoms: 1.22 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: 1.06 Conformation dependent library (CDL) restraints added in 518.5 milliseconds 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: 0.45 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: 1.14 Time building geometry restraints manager: 1.21 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: 5.250 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.890 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- 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 (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 (0.36), 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 TRP 0.055 0.016 TRP A 575 HIS 0.016 0.004 HIS A 436 PHE 0.047 0.009 PHE A 265 TYR 0.067 0.014 TYR A 335 ARG 0.008 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.19579 ( 154) hydrogen bonds : angle 8.13867 ( 432) metal coordination : bond 0.21498 ( 2) covalent geometry : bond 0.01202 ( 4065) covalent geometry : angle 1.58181 ( 5521) 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 : 0.456 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: 0.6843 (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: 0.6529 (mtp180) REVERT: A 483 ASN cc_start: 0.7222 (t0) cc_final: 0.6603 (t0) REVERT: A 523 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7204 (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: 0.6099 (mtm180) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.2404 time to fit residues: 27.5956 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 : 0.432 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.0970 chunk 37 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 25 optimal weight: 0.0270 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.0980 chunk 29 optimal weight: 0.4980 chunk 45 optimal weight: 0.2980 overall best weight: 0.1236 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116148 restraints weight = 5606.793| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.23 r_work: 0.3246 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1905 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= 0.131 Angle : 0.595 9.854 5521 Z= 0.308 Chirality : 0.041 0.132 589 Planarity : 0.005 0.047 723 Dihedral : 5.492 54.986 563 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.67 % Allowed : 10.19 % Favored : 87.14 % 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: 0.38 (0.37), residues: 493 helix: 1.32 (0.41), residues: 143 sheet: 0.46 (0.52), residues: 93 loop : -0.39 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 57 HIS 0.003 0.001 HIS A 192 PHE 0.015 0.002 PHE A 153 TYR 0.014 0.002 TYR A 335 ARG 0.004 0.001 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 154) hydrogen bonds : angle 5.80454 ( 432) metal coordination : bond 0.00663 ( 2) covalent geometry : bond 0.00302 ( 4065) covalent geometry : angle 0.59470 ( 5521) Misc. bond : bond 0.00015 ( 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 77 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7678 (mm110) cc_final: 0.7150 (pt0) REVERT: A 316 LEU cc_start: 0.9143 (mt) cc_final: 0.8651 (mt) REVERT: A 459 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8432 (ttm) REVERT: A 483 ASN cc_start: 0.7499 (t0) cc_final: 0.7170 (t0) REVERT: A 598 ARG cc_start: 0.7426 (mmm160) cc_final: 0.7030 (mtm180) outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 0.1870 time to fit residues: 16.5786 Evaluate side-chains 57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 528 ILE 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 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 22 optimal weight: 0.2980 chunk 48 optimal weight: 0.0980 chunk 28 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 0.0770 chunk 14 optimal weight: 0.4980 overall best weight: 0.1496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 226 GLN A 323 HIS A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112630 restraints weight = 5666.059| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.26 r_work: 0.3120 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2517 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= 0.131 Angle : 0.551 8.714 5521 Z= 0.281 Chirality : 0.041 0.127 589 Planarity : 0.004 0.039 723 Dihedral : 5.248 54.103 563 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.16 % Allowed : 11.65 % Favored : 85.19 % 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: 0.50 (0.38), residues: 493 helix: 1.47 (0.42), residues: 144 sheet: 0.59 (0.53), residues: 93 loop : -0.38 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 119 HIS 0.004 0.001 HIS A 192 PHE 0.019 0.002 PHE A 546 TYR 0.013 0.002 TYR A 519 ARG 0.003 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 154) hydrogen bonds : angle 5.20636 ( 432) metal coordination : bond 0.00179 ( 2) covalent geometry : bond 0.00314 ( 4065) covalent geometry : angle 0.55080 ( 5521) Misc. bond : bond 0.00007 ( 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 69 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7527 (mm110) cc_final: 0.7061 (pt0) REVERT: A 316 LEU cc_start: 0.9182 (mt) cc_final: 0.8600 (mt) REVERT: A 483 ASN cc_start: 0.7352 (t0) cc_final: 0.7117 (t0) REVERT: A 519 TYR cc_start: 0.8655 (m-80) cc_final: 0.8036 (m-80) REVERT: A 598 ARG cc_start: 0.7490 (mmm160) cc_final: 0.7018 (mtm180) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 0.1828 time to fit residues: 14.5196 Evaluate side-chains 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 206 ASP 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 A residue 599 ASN 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 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 5 optimal weight: 0.0870 chunk 3 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 38 optimal weight: 0.3980 chunk 1 optimal weight: 0.3980 chunk 29 optimal weight: 0.1980 chunk 19 optimal weight: 0.1980 chunk 0 optimal weight: 0.0980 overall best weight: 0.0932 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.123730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113223 restraints weight = 5716.005| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.27 r_work: 0.3203 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4068 Z= 0.111 Angle : 0.530 7.758 5521 Z= 0.268 Chirality : 0.040 0.131 589 Planarity : 0.004 0.034 723 Dihedral : 5.051 51.404 563 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.18 % Allowed : 12.14 % Favored : 85.68 % 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: 0.60 (0.38), residues: 493 helix: 1.46 (0.42), residues: 146 sheet: 0.69 (0.53), residues: 93 loop : -0.30 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 119 HIS 0.003 0.001 HIS A 192 PHE 0.017 0.002 PHE A 546 TYR 0.010 0.001 TYR A 519 ARG 0.002 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 154) hydrogen bonds : angle 5.07116 ( 432) metal coordination : bond 0.00143 ( 2) covalent geometry : bond 0.00258 ( 4065) covalent geometry : angle 0.52978 ( 5521) Misc. bond : bond 0.00003 ( 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 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7474 (mm110) cc_final: 0.7051 (pt0) REVERT: A 316 LEU cc_start: 0.9204 (mt) cc_final: 0.8597 (mt) REVERT: A 459 MET cc_start: 0.8671 (ttm) cc_final: 0.8466 (ttm) REVERT: A 464 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8917 (mt) REVERT: A 483 ASN cc_start: 0.7368 (t0) cc_final: 0.7082 (t0) REVERT: A 519 TYR cc_start: 0.8615 (m-80) cc_final: 0.7877 (m-80) REVERT: A 598 ARG cc_start: 0.7436 (mmm160) cc_final: 0.6940 (mtm180) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.1781 time to fit residues: 11.9444 Evaluate side-chains 50 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 206 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 568 ASP 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 1 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 47 optimal weight: 0.0000 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 22 optimal weight: 0.0770 chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 0.0670 overall best weight: 0.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 214 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 = 0.3426 r_free = 0.3426 target = 0.125421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114889 restraints weight = 5804.106| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.28 r_work: 0.3210 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4068 Z= 0.093 Angle : 0.495 7.412 5521 Z= 0.249 Chirality : 0.039 0.148 589 Planarity : 0.004 0.033 723 Dihedral : 4.629 40.936 563 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.16 % Allowed : 11.89 % Favored : 84.95 % 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: 0.69 (0.38), residues: 493 helix: 1.50 (0.42), residues: 146 sheet: 0.82 (0.55), residues: 93 loop : -0.26 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 119 HIS 0.002 0.001 HIS A 192 PHE 0.014 0.001 PHE A 546 TYR 0.009 0.001 TYR A 157 ARG 0.003 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 154) hydrogen bonds : angle 4.89244 ( 432) metal coordination : bond 0.00124 ( 2) covalent geometry : bond 0.00219 ( 4065) covalent geometry : angle 0.49542 ( 5521) Misc. bond : bond 0.00016 ( 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 65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7556 (mm110) cc_final: 0.7283 (pt0) REVERT: A 316 LEU cc_start: 0.9192 (mt) cc_final: 0.8586 (mt) REVERT: A 440 ARG cc_start: 0.7762 (mtm110) cc_final: 0.7191 (mtp180) REVERT: A 464 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8955 (mt) REVERT: A 483 ASN cc_start: 0.7318 (t0) cc_final: 0.6980 (t0) REVERT: A 519 TYR cc_start: 0.8554 (m-80) cc_final: 0.7739 (m-80) REVERT: A 598 ARG cc_start: 0.7471 (mmm160) cc_final: 0.7023 (mtm180) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.1676 time to fit residues: 13.2518 Evaluate side-chains 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 464 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.0870 chunk 1 optimal weight: 0.0040 chunk 30 optimal weight: 0.2980 chunk 46 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 45 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 overall best weight: 0.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 455 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 = 0.3423 r_free = 0.3423 target = 0.125328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114835 restraints weight = 5641.247| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.26 r_work: 0.3221 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4068 Z= 0.092 Angle : 0.493 7.657 5521 Z= 0.246 Chirality : 0.039 0.135 589 Planarity : 0.004 0.031 723 Dihedral : 4.470 35.781 563 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.67 % Allowed : 12.62 % Favored : 84.71 % 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: 0.74 (0.38), residues: 493 helix: 1.58 (0.43), residues: 146 sheet: 0.82 (0.55), residues: 93 loop : -0.24 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 119 HIS 0.002 0.001 HIS A 596 PHE 0.012 0.001 PHE A 546 TYR 0.008 0.001 TYR A 157 ARG 0.003 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 154) hydrogen bonds : angle 4.86704 ( 432) metal coordination : bond 0.00111 ( 2) covalent geometry : bond 0.00219 ( 4065) covalent geometry : angle 0.49252 ( 5521) Misc. bond : bond 0.00023 ( 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 61 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7546 (mm110) cc_final: 0.7271 (pt0) REVERT: A 440 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7180 (mtp180) REVERT: A 464 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8959 (mt) REVERT: A 483 ASN cc_start: 0.7331 (t0) cc_final: 0.7054 (t0) REVERT: A 519 TYR cc_start: 0.8543 (m-80) cc_final: 0.7697 (m-80) REVERT: A 598 ARG cc_start: 0.7441 (mmm160) cc_final: 0.6913 (mtm180) outliers start: 11 outliers final: 10 residues processed: 60 average time/residue: 0.1629 time to fit residues: 12.4199 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 309 VAL 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 11 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 9 optimal weight: 0.0370 chunk 17 optimal weight: 0.4980 overall best weight: 0.1256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112515 restraints weight = 5693.170| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.28 r_work: 0.3193 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4068 Z= 0.111 Angle : 0.505 7.778 5521 Z= 0.252 Chirality : 0.040 0.142 589 Planarity : 0.004 0.029 723 Dihedral : 4.400 32.482 563 Min Nonbonded Distance : 2.003 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 (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: 0.68 (0.38), residues: 493 helix: 1.54 (0.43), residues: 146 sheet: 0.72 (0.53), residues: 100 loop : -0.27 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 119 HIS 0.003 0.001 HIS A 596 PHE 0.011 0.001 PHE A 245 TYR 0.009 0.001 TYR A 519 ARG 0.007 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 154) hydrogen bonds : angle 4.85653 ( 432) metal coordination : bond 0.00237 ( 2) covalent geometry : bond 0.00272 ( 4065) covalent geometry : angle 0.50484 ( 5521) Misc. bond : bond 0.00011 ( 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 59 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7548 (mm110) cc_final: 0.7298 (pt0) REVERT: A 226 GLN cc_start: 0.7459 (mt0) cc_final: 0.7157 (mt0) REVERT: A 316 LEU cc_start: 0.9056 (mt) cc_final: 0.8605 (mt) REVERT: A 440 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7190 (mtp180) REVERT: A 464 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8962 (mt) REVERT: A 483 ASN cc_start: 0.7371 (t0) cc_final: 0.7119 (t0) REVERT: A 519 TYR cc_start: 0.8611 (m-80) cc_final: 0.7773 (m-80) REVERT: A 598 ARG cc_start: 0.7472 (mmm160) cc_final: 0.6927 (mtm180) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.1697 time to fit residues: 12.3006 Evaluate side-chains 57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 309 VAL 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 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 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.0570 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 47 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 2 optimal weight: 0.0870 chunk 49 optimal weight: 0.3980 overall best weight: 0.1432 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.121299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110512 restraints weight = 5693.770| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.27 r_work: 0.3163 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4068 Z= 0.120 Angle : 0.520 8.303 5521 Z= 0.259 Chirality : 0.040 0.157 589 Planarity : 0.004 0.027 723 Dihedral : 4.341 25.741 563 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.67 % Allowed : 14.08 % Favored : 83.25 % 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: 0.65 (0.38), residues: 493 helix: 1.40 (0.42), residues: 146 sheet: 0.83 (0.54), residues: 100 loop : -0.28 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 57 HIS 0.002 0.001 HIS A 471 PHE 0.012 0.001 PHE A 268 TYR 0.011 0.001 TYR A 519 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 154) hydrogen bonds : angle 4.82372 ( 432) metal coordination : bond 0.00294 ( 2) covalent geometry : bond 0.00293 ( 4065) covalent geometry : angle 0.52045 ( 5521) Misc. bond : bond 0.00008 ( 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 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.429 Fit side-chains REVERT: A 226 GLN cc_start: 0.7642 (mt0) cc_final: 0.7375 (mt0) REVERT: A 316 LEU cc_start: 0.9057 (mt) cc_final: 0.8587 (mt) REVERT: A 440 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7414 (mtp180) REVERT: A 464 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8935 (mt) REVERT: A 483 ASN cc_start: 0.7348 (t0) cc_final: 0.7042 (t0) REVERT: A 519 TYR cc_start: 0.8660 (m-80) cc_final: 0.7828 (m-80) REVERT: A 556 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: A 598 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7126 (mtm180) outliers start: 11 outliers final: 8 residues processed: 56 average time/residue: 0.2018 time to fit residues: 13.8498 Evaluate side-chains 59 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 309 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 8 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 27 optimal weight: 0.2980 chunk 14 optimal weight: 0.0980 overall best weight: 0.1254 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.121581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.110724 restraints weight = 5820.261| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.30 r_work: 0.3161 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4068 Z= 0.117 Angle : 0.518 8.154 5521 Z= 0.258 Chirality : 0.040 0.147 589 Planarity : 0.004 0.026 723 Dihedral : 4.187 18.253 560 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 (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: 0.62 (0.38), residues: 493 helix: 1.37 (0.42), residues: 146 sheet: 0.84 (0.53), residues: 100 loop : -0.30 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 57 HIS 0.002 0.001 HIS A 596 PHE 0.028 0.002 PHE A 546 TYR 0.011 0.001 TYR A 519 ARG 0.007 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 154) hydrogen bonds : angle 4.84811 ( 432) metal coordination : bond 0.00223 ( 2) covalent geometry : bond 0.00289 ( 4065) covalent geometry : angle 0.51755 ( 5521) Misc. bond : bond 0.00004 ( 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 : 0.453 Fit side-chains REVERT: A 226 GLN cc_start: 0.7664 (mt0) cc_final: 0.7401 (mt0) REVERT: A 316 LEU cc_start: 0.9052 (mt) cc_final: 0.8578 (mt) REVERT: A 440 ARG cc_start: 0.7788 (mtm110) cc_final: 0.7250 (mtp180) REVERT: A 464 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8945 (mt) REVERT: A 483 ASN cc_start: 0.7339 (t0) cc_final: 0.7063 (t0) REVERT: A 519 TYR cc_start: 0.8663 (m-80) cc_final: 0.7820 (m-80) REVERT: A 546 PHE cc_start: 0.6420 (p90) cc_final: 0.5287 (m-80) REVERT: A 556 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: A 598 ARG cc_start: 0.7604 (mmm160) cc_final: 0.6966 (mtm180) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 0.1956 time to fit residues: 13.9531 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 309 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.0770 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 2 optimal weight: 0.0570 chunk 46 optimal weight: 0.0980 chunk 36 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 overall best weight: 0.0852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111755 restraints weight = 5750.541| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.29 r_work: 0.3175 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3522 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= 0.104 Angle : 0.531 8.118 5521 Z= 0.263 Chirality : 0.040 0.147 589 Planarity : 0.004 0.056 723 Dihedral : 4.158 17.484 560 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.18 % Allowed : 14.32 % Favored : 83.50 % 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: 0.65 (0.39), residues: 493 helix: 1.39 (0.43), residues: 146 sheet: 0.84 (0.54), residues: 100 loop : -0.28 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 592 HIS 0.002 0.001 HIS A 596 PHE 0.028 0.002 PHE A 546 TYR 0.009 0.001 TYR A 519 ARG 0.014 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 154) hydrogen bonds : angle 4.85280 ( 432) metal coordination : bond 0.00155 ( 2) covalent geometry : bond 0.00253 ( 4065) covalent geometry : angle 0.53086 ( 5521) Misc. bond : bond 0.00011 ( 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 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.441 Fit side-chains REVERT: A 226 GLN cc_start: 0.7627 (mt0) cc_final: 0.7359 (mt0) REVERT: A 316 LEU cc_start: 0.9041 (mt) cc_final: 0.8567 (mt) REVERT: A 322 LEU cc_start: 0.8467 (mp) cc_final: 0.7973 (mt) REVERT: A 440 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7271 (mtp180) REVERT: A 464 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8960 (mt) REVERT: A 483 ASN cc_start: 0.7310 (t0) cc_final: 0.7023 (t0) REVERT: A 519 TYR cc_start: 0.8639 (m-80) cc_final: 0.7794 (m-80) REVERT: A 546 PHE cc_start: 0.6444 (p90) cc_final: 0.5286 (m-80) REVERT: A 556 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: A 598 ARG cc_start: 0.7573 (mmm160) cc_final: 0.6928 (mtm180) outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.2101 time to fit residues: 14.7036 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 309 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7697 > 50: distance: 34 - 38: 29.348 distance: 38 - 39: 18.774 distance: 39 - 40: 48.228 distance: 39 - 42: 14.822 distance: 40 - 47: 35.721 distance: 42 - 43: 5.958 distance: 43 - 44: 14.235 distance: 44 - 45: 42.219 distance: 44 - 46: 42.309 distance: 47 - 48: 35.959 distance: 47 - 53: 41.102 distance: 48 - 49: 24.366 distance: 48 - 51: 19.777 distance: 49 - 50: 10.994 distance: 49 - 54: 4.507 distance: 51 - 52: 12.008 distance: 52 - 53: 34.027 distance: 54 - 55: 13.808 distance: 55 - 56: 9.996 distance: 55 - 58: 23.133 distance: 56 - 57: 28.218 distance: 56 - 65: 25.748 distance: 58 - 59: 3.415 distance: 59 - 60: 22.901 distance: 60 - 61: 28.475 distance: 61 - 62: 11.753 distance: 62 - 63: 8.213 distance: 62 - 64: 6.275 distance: 65 - 66: 41.099 distance: 66 - 67: 29.953 distance: 66 - 69: 22.830 distance: 67 - 68: 12.648 distance: 67 - 73: 17.481 distance: 69 - 70: 14.266 distance: 70 - 71: 23.488 distance: 70 - 72: 23.767 distance: 73 - 74: 50.768 distance: 74 - 75: 34.464 distance: 75 - 76: 21.318 distance: 75 - 78: 20.786 distance: 78 - 79: 17.447 distance: 79 - 80: 12.628 distance: 79 - 82: 8.127 distance: 80 - 87: 16.313 distance: 82 - 83: 22.242 distance: 83 - 84: 13.941 distance: 84 - 85: 11.966 distance: 84 - 86: 18.593 distance: 87 - 88: 23.111 distance: 88 - 89: 44.795 distance: 88 - 91: 12.244 distance: 89 - 90: 55.778 distance: 89 - 95: 19.056 distance: 91 - 92: 40.440 distance: 92 - 93: 30.264 distance: 92 - 94: 19.605 distance: 95 - 96: 50.433 distance: 96 - 97: 23.170 distance: 96 - 99: 33.067 distance: 97 - 98: 19.204 distance: 97 - 106: 45.454 distance: 99 - 100: 46.486 distance: 100 - 101: 32.172 distance: 100 - 102: 52.264 distance: 102 - 104: 6.587 distance: 103 - 105: 50.631 distance: 104 - 105: 40.459 distance: 106 - 107: 28.646 distance: 106 - 112: 19.779 distance: 107 - 108: 23.697 distance: 107 - 110: 50.185 distance: 108 - 109: 22.545 distance: 108 - 113: 14.770 distance: 111 - 112: 31.034 distance: 113 - 114: 27.623 distance: 114 - 115: 21.834 distance: 114 - 117: 21.882 distance: 115 - 116: 17.686 distance: 115 - 121: 26.006 distance: 117 - 118: 32.828 distance: 118 - 119: 38.540 distance: 118 - 120: 19.320 distance: 175 - 180: 3.153