Starting phenix.real_space_refine on Fri Aug 22 22:02:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twi_41668/08_2025/8twi_41668.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twi_41668/08_2025/8twi_41668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8twi_41668/08_2025/8twi_41668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twi_41668/08_2025/8twi_41668.map" model { file = "/net/cci-nas-00/data/ceres_data/8twi_41668/08_2025/8twi_41668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twi_41668/08_2025/8twi_41668.cif" } resolution = 2.69 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= 0.000 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 1 6.06 5 S 26 5.16 5 C 2584 2.51 5 N 696 2.21 5 O 765 1.98 5 H 4023 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 8096 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3096 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "C" Number of atoms: 4696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4696 Classifications: {'peptide': 297} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 284} Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 302 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.73, per 1000 atoms: 0.21 Number of scatterers: 8096 At special positions: 0 Unit cell: (77.43, 72.624, 86.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 S 26 16.00 O 765 8.00 N 696 7.00 C 2584 6.00 H 4023 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 268.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 59 " 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 65.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.875A pdb=" N LEU A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.587A pdb=" N TYR A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.560A pdb=" N LEU A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 482 removed outlier: 3.792A pdb=" N LYS A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N GLU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.610A pdb=" N ALA A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 520 removed outlier: 3.502A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.658A pdb=" N ILE A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.627A pdb=" N VAL C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.677A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 removed outlier: 3.600A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.801A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.664A pdb=" N GLU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.204A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 220 hydrogen bonds defined for protein. 639 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: 1.78 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4010 1.03 - 1.23: 13 1.23 - 1.42: 1739 1.42 - 1.61: 2378 1.61 - 1.81: 39 Bond restraints: 8179 Sorted by residual: bond pdb=" N GLY D 93 " pdb=" CA GLY D 93 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.75e+00 bond pdb=" N GLY A 396 " pdb=" CA GLY A 396 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.40e+00 bond pdb=" N ASP C 2 " pdb=" CA ASP C 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N GLY D 93 " pdb=" H GLY D 93 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" N GLY A 396 " pdb=" H GLY A 396 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 8174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 14035 1.12 - 2.24: 701 2.24 - 3.36: 21 3.36 - 4.48: 14 4.48 - 5.60: 4 Bond angle restraints: 14775 Sorted by residual: angle pdb=" N HIS C 241 " pdb=" CA HIS C 241 " pdb=" CB HIS C 241 " ideal model delta sigma weight residual 114.27 108.67 5.60 1.64e+00 3.72e-01 1.17e+01 angle pdb=" C ARG C 239 " pdb=" N ALA C 240 " pdb=" CA ALA C 240 " ideal model delta sigma weight residual 122.16 125.63 -3.47 1.32e+00 5.74e-01 6.91e+00 angle pdb=" N LEU C 282 " pdb=" CA LEU C 282 " pdb=" CB LEU C 282 " ideal model delta sigma weight residual 113.65 110.06 3.59 1.47e+00 4.63e-01 5.97e+00 angle pdb=" C ALA C 240 " pdb=" N HIS C 241 " pdb=" CA HIS C 241 " ideal model delta sigma weight residual 125.66 121.96 3.70 1.85e+00 2.92e-01 4.01e+00 angle pdb=" CA VAL C 58 " pdb=" C VAL C 58 " pdb=" N HIS C 59 " ideal model delta sigma weight residual 116.60 119.10 -2.50 1.45e+00 4.76e-01 2.97e+00 ... (remaining 14770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 3569 16.80 - 33.60: 152 33.60 - 50.39: 72 50.39 - 67.19: 32 67.19 - 83.99: 12 Dihedral angle restraints: 3837 sinusoidal: 2094 harmonic: 1743 Sorted by residual: dihedral pdb=" CA ALA C 240 " pdb=" C ALA C 240 " pdb=" N HIS C 241 " pdb=" CA HIS C 241 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TYR C 127 " pdb=" C TYR C 127 " pdb=" N GLY C 128 " pdb=" CA GLY C 128 " ideal model delta harmonic sigma weight residual 180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA SER C 238 " pdb=" C SER C 238 " pdb=" N ARG C 239 " pdb=" CA ARG C 239 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 418 0.026 - 0.052: 120 0.052 - 0.078: 55 0.078 - 0.104: 24 0.104 - 0.130: 12 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA VAL C 237 " pdb=" N VAL C 237 " pdb=" C VAL C 237 " pdb=" CB VAL C 237 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL C 45 " pdb=" N VAL C 45 " pdb=" C VAL C 45 " pdb=" CB VAL C 45 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE C 275 " pdb=" N ILE C 275 " pdb=" C ILE C 275 " pdb=" CB ILE C 275 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.26e-01 ... (remaining 626 not shown) Planarity restraints: 1215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 538 " -0.012 2.00e-02 2.50e+03 7.57e-03 1.72e+00 pdb=" CG PHE A 538 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 538 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 538 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 538 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 538 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 538 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 189 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO C 190 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 240 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C ALA C 240 " -0.018 2.00e-02 2.50e+03 pdb=" O ALA C 240 " 0.007 2.00e-02 2.50e+03 pdb=" N HIS C 241 " 0.006 2.00e-02 2.50e+03 ... (remaining 1212 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 264 2.15 - 2.76: 15414 2.76 - 3.37: 23905 3.37 - 3.99: 30526 3.99 - 4.60: 48717 Nonbonded interactions: 118826 Sorted by model distance: nonbonded pdb=" HG SER C 120 " pdb=" OE2 GLU C 188 " model vdw 1.535 2.450 nonbonded pdb=" O VAL C 94 " pdb=" HG1 THR C 98 " model vdw 1.619 2.450 nonbonded pdb=" O GLY C 73 " pdb=" HH TYR C 80 " model vdw 1.619 2.450 nonbonded pdb=" O GLU A 565 " pdb=" HG1 THR A 568 " model vdw 1.637 2.450 nonbonded pdb=" OD1 ASP C 202 " pdb="HH21 ARG C 239 " model vdw 1.648 2.450 ... (remaining 118821 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: 14.020 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: 0.050 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.730 Find NCS groups from input model: 0.030 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.002 0.042 4157 Z= 0.110 Angle : 0.460 5.602 5633 Z= 0.255 Chirality : 0.036 0.130 629 Planarity : 0.003 0.030 728 Dihedral : 9.781 83.990 1539 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.67 % Allowed : 0.22 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.15 (0.38), residues: 504 helix: 1.17 (0.31), residues: 285 sheet: 0.20 (0.90), residues: 36 loop : 0.43 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 527 TYR 0.009 0.001 TYR C 127 PHE 0.022 0.001 PHE A 538 TRP 0.005 0.001 TRP A 417 HIS 0.005 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 4156) covalent geometry : angle 0.45953 ( 5633) hydrogen bonds : bond 0.20275 ( 220) hydrogen bonds : angle 7.05114 ( 639) metal coordination : bond 0.00420 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 GLN cc_start: 0.9177 (tt0) cc_final: 0.8851 (tt0) REVERT: A 555 THR cc_start: 0.9603 (m) cc_final: 0.9123 (p) REVERT: A 558 SER cc_start: 0.9482 (t) cc_final: 0.9222 (p) REVERT: C 197 ASP cc_start: 0.8834 (m-30) cc_final: 0.8421 (m-30) REVERT: C 238 SER cc_start: 0.9108 (t) cc_final: 0.8734 (p) outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 0.8338 time to fit residues: 75.9323 Evaluate side-chains 58 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.075409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.053963 restraints weight = 30485.476| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.36 r_work: 0.2761 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4157 Z= 0.156 Angle : 0.591 7.431 5633 Z= 0.314 Chirality : 0.040 0.130 629 Planarity : 0.005 0.062 728 Dihedral : 4.756 31.653 556 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.22 % Allowed : 9.40 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.20 (0.38), residues: 504 helix: 1.37 (0.31), residues: 291 sheet: -0.19 (0.94), residues: 37 loop : 0.21 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.011 0.001 TYR C 265 PHE 0.023 0.001 PHE A 538 TRP 0.005 0.001 TRP A 417 HIS 0.003 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4156) covalent geometry : angle 0.59102 ( 5633) hydrogen bonds : bond 0.05694 ( 220) hydrogen bonds : angle 5.05543 ( 639) metal coordination : bond 0.00204 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8710 (m) cc_final: 0.8373 (p) REVERT: A 514 GLN cc_start: 0.9040 (tt0) cc_final: 0.8590 (tt0) REVERT: A 517 THR cc_start: 0.9499 (m) cc_final: 0.9069 (p) REVERT: A 531 ASP cc_start: 0.8545 (t0) cc_final: 0.8294 (t0) REVERT: A 558 SER cc_start: 0.9483 (t) cc_final: 0.9200 (p) REVERT: A 570 ASP cc_start: 0.8873 (t0) cc_final: 0.8266 (t0) REVERT: C 191 HIS cc_start: 0.8286 (m90) cc_final: 0.7919 (m-70) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.9012 time to fit residues: 59.4609 Evaluate side-chains 55 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053138 restraints weight = 31301.413| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.43 r_work: 0.2745 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4157 Z= 0.158 Angle : 0.541 6.152 5633 Z= 0.287 Chirality : 0.039 0.131 629 Planarity : 0.004 0.027 728 Dihedral : 4.339 19.752 554 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.45 % Allowed : 10.07 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.35 (0.38), residues: 504 helix: 1.48 (0.31), residues: 299 sheet: -0.22 (0.91), residues: 37 loop : 0.26 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.008 0.001 TYR C 265 PHE 0.021 0.001 PHE A 538 TRP 0.007 0.001 TRP A 417 HIS 0.004 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4156) covalent geometry : angle 0.54075 ( 5633) hydrogen bonds : bond 0.04657 ( 220) hydrogen bonds : angle 4.73320 ( 639) metal coordination : bond 0.00243 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8682 (m) cc_final: 0.8351 (p) REVERT: A 517 THR cc_start: 0.9485 (m) cc_final: 0.9095 (p) REVERT: A 531 ASP cc_start: 0.8575 (t0) cc_final: 0.8270 (t0) REVERT: A 558 SER cc_start: 0.9516 (t) cc_final: 0.9243 (p) REVERT: A 570 ASP cc_start: 0.8731 (t0) cc_final: 0.8340 (t0) REVERT: C 191 HIS cc_start: 0.8360 (m90) cc_final: 0.7988 (m-70) REVERT: C 238 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8264 (p) REVERT: C 242 GLN cc_start: 0.8998 (tt0) cc_final: 0.8673 (tt0) outliers start: 2 outliers final: 0 residues processed: 61 average time/residue: 0.9592 time to fit residues: 61.0209 Evaluate side-chains 53 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.053983 restraints weight = 31506.670| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.43 r_work: 0.2758 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4157 Z= 0.119 Angle : 0.528 5.822 5633 Z= 0.275 Chirality : 0.038 0.127 629 Planarity : 0.004 0.048 728 Dihedral : 4.175 19.564 554 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.22 % Allowed : 11.19 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.53 (0.39), residues: 504 helix: 1.64 (0.31), residues: 299 sheet: -0.20 (0.90), residues: 37 loop : 0.34 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 527 TYR 0.006 0.001 TYR C 265 PHE 0.022 0.001 PHE A 538 TRP 0.007 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4156) covalent geometry : angle 0.52811 ( 5633) hydrogen bonds : bond 0.04065 ( 220) hydrogen bonds : angle 4.50388 ( 639) metal coordination : bond 0.00142 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ASN cc_start: 0.8726 (t0) cc_final: 0.8463 (t0) REVERT: A 512 CYS cc_start: 0.8740 (m) cc_final: 0.8343 (p) REVERT: A 517 THR cc_start: 0.9489 (m) cc_final: 0.9115 (p) REVERT: A 531 ASP cc_start: 0.8517 (t70) cc_final: 0.8187 (t0) REVERT: A 558 SER cc_start: 0.9533 (t) cc_final: 0.9260 (p) REVERT: A 570 ASP cc_start: 0.8744 (t0) cc_final: 0.8330 (t0) REVERT: C 191 HIS cc_start: 0.8354 (m90) cc_final: 0.7993 (m-70) REVERT: C 197 ASP cc_start: 0.8938 (m-30) cc_final: 0.8596 (m-30) REVERT: C 242 GLN cc_start: 0.9003 (tt0) cc_final: 0.8787 (tt0) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.9797 time to fit residues: 52.1386 Evaluate side-chains 49 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.074454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.053062 restraints weight = 31743.743| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.45 r_work: 0.2741 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4157 Z= 0.152 Angle : 0.525 6.480 5633 Z= 0.275 Chirality : 0.038 0.134 629 Planarity : 0.004 0.046 728 Dihedral : 4.119 19.046 554 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.45 % Allowed : 11.41 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.48 (0.39), residues: 504 helix: 1.57 (0.31), residues: 301 sheet: -0.23 (0.88), residues: 37 loop : 0.34 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 527 TYR 0.006 0.001 TYR C 265 PHE 0.022 0.001 PHE A 538 TRP 0.007 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4156) covalent geometry : angle 0.52496 ( 5633) hydrogen bonds : bond 0.03929 ( 220) hydrogen bonds : angle 4.43345 ( 639) metal coordination : bond 0.00233 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8718 (m) cc_final: 0.8368 (p) REVERT: A 517 THR cc_start: 0.9480 (m) cc_final: 0.9127 (p) REVERT: A 531 ASP cc_start: 0.8531 (t70) cc_final: 0.8200 (t0) REVERT: A 558 SER cc_start: 0.9536 (t) cc_final: 0.9262 (p) REVERT: A 570 ASP cc_start: 0.8765 (t0) cc_final: 0.8398 (t0) REVERT: C 191 HIS cc_start: 0.8407 (m90) cc_final: 0.8046 (m-70) REVERT: C 197 ASP cc_start: 0.8934 (m-30) cc_final: 0.8584 (m-30) REVERT: C 242 GLN cc_start: 0.9015 (tt0) cc_final: 0.8430 (mt0) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.9373 time to fit residues: 47.8073 Evaluate side-chains 48 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.074253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052637 restraints weight = 31299.259| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.46 r_work: 0.2745 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4157 Z= 0.134 Angle : 0.506 5.939 5633 Z= 0.265 Chirality : 0.038 0.131 629 Planarity : 0.004 0.050 728 Dihedral : 4.034 18.792 554 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.45 % Allowed : 12.30 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.56 (0.39), residues: 504 helix: 1.63 (0.31), residues: 301 sheet: -0.13 (0.87), residues: 37 loop : 0.37 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.006 0.001 TYR C 265 PHE 0.022 0.001 PHE A 538 TRP 0.007 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4156) covalent geometry : angle 0.50551 ( 5633) hydrogen bonds : bond 0.03726 ( 220) hydrogen bonds : angle 4.33559 ( 639) metal coordination : bond 0.00213 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8755 (m) cc_final: 0.8394 (p) REVERT: A 517 THR cc_start: 0.9484 (m) cc_final: 0.9139 (p) REVERT: A 531 ASP cc_start: 0.8508 (t70) cc_final: 0.8200 (t0) REVERT: A 558 SER cc_start: 0.9535 (t) cc_final: 0.9253 (p) REVERT: A 570 ASP cc_start: 0.8785 (t0) cc_final: 0.8409 (t0) REVERT: C 191 HIS cc_start: 0.8430 (m90) cc_final: 0.8074 (m-70) REVERT: C 197 ASP cc_start: 0.8933 (m-30) cc_final: 0.8593 (m-30) REVERT: D 100 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7502 (mm-30) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.9567 time to fit residues: 47.7115 Evaluate side-chains 47 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.073372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.051547 restraints weight = 32082.635| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.50 r_work: 0.2715 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4157 Z= 0.187 Angle : 0.522 5.044 5633 Z= 0.278 Chirality : 0.039 0.135 629 Planarity : 0.004 0.053 728 Dihedral : 4.094 18.599 554 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.67 % Allowed : 12.98 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.51 (0.39), residues: 504 helix: 1.59 (0.31), residues: 301 sheet: -0.09 (0.87), residues: 37 loop : 0.34 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.006 0.001 TYR C 265 PHE 0.022 0.002 PHE A 538 TRP 0.007 0.001 TRP A 417 HIS 0.004 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 4156) covalent geometry : angle 0.52182 ( 5633) hydrogen bonds : bond 0.03944 ( 220) hydrogen bonds : angle 4.41097 ( 639) metal coordination : bond 0.00354 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.8553 (t70) cc_final: 0.8261 (t0) REVERT: A 558 SER cc_start: 0.9530 (t) cc_final: 0.9249 (p) REVERT: A 570 ASP cc_start: 0.8793 (t0) cc_final: 0.8435 (t0) REVERT: C 191 HIS cc_start: 0.8478 (m90) cc_final: 0.8101 (m-70) REVERT: C 197 ASP cc_start: 0.8952 (m-30) cc_final: 0.8611 (m-30) REVERT: C 242 GLN cc_start: 0.9017 (tt0) cc_final: 0.8723 (mt0) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 1.0019 time to fit residues: 48.9893 Evaluate side-chains 47 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.074274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.052811 restraints weight = 31419.924| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.40 r_work: 0.2735 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4157 Z= 0.138 Angle : 0.512 5.904 5633 Z= 0.270 Chirality : 0.038 0.129 629 Planarity : 0.004 0.054 728 Dihedral : 4.032 18.522 554 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.45 % Allowed : 13.87 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.59 (0.39), residues: 504 helix: 1.71 (0.31), residues: 299 sheet: -0.18 (0.87), residues: 37 loop : 0.30 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 527 TYR 0.006 0.001 TYR A 495 PHE 0.022 0.001 PHE A 538 TRP 0.008 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4156) covalent geometry : angle 0.51154 ( 5633) hydrogen bonds : bond 0.03672 ( 220) hydrogen bonds : angle 4.31266 ( 639) metal coordination : bond 0.00234 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8721 (m) cc_final: 0.8382 (p) REVERT: A 531 ASP cc_start: 0.8500 (t70) cc_final: 0.8253 (t0) REVERT: A 558 SER cc_start: 0.9528 (t) cc_final: 0.9246 (p) REVERT: A 570 ASP cc_start: 0.8797 (t0) cc_final: 0.8308 (t0) REVERT: C 191 HIS cc_start: 0.8468 (m90) cc_final: 0.8092 (m-70) REVERT: C 197 ASP cc_start: 0.8945 (m-30) cc_final: 0.8605 (m-30) REVERT: C 242 GLN cc_start: 0.9027 (tt0) cc_final: 0.8694 (mt0) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.9519 time to fit residues: 47.5240 Evaluate side-chains 46 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.052174 restraints weight = 31903.461| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.47 r_work: 0.2731 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4157 Z= 0.149 Angle : 0.524 6.137 5633 Z= 0.274 Chirality : 0.038 0.130 629 Planarity : 0.004 0.055 728 Dihedral : 4.000 18.259 554 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.45 % Allowed : 14.09 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.65 (0.39), residues: 504 helix: 1.69 (0.31), residues: 301 sheet: -0.07 (0.87), residues: 37 loop : 0.41 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.007 0.001 TYR C 265 PHE 0.022 0.001 PHE A 538 TRP 0.007 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4156) covalent geometry : angle 0.52429 ( 5633) hydrogen bonds : bond 0.03708 ( 220) hydrogen bonds : angle 4.32225 ( 639) metal coordination : bond 0.00257 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 CYS cc_start: 0.8694 (m) cc_final: 0.8395 (p) REVERT: A 531 ASP cc_start: 0.8506 (t70) cc_final: 0.8302 (t0) REVERT: A 558 SER cc_start: 0.9531 (t) cc_final: 0.9250 (p) REVERT: A 570 ASP cc_start: 0.8793 (t0) cc_final: 0.8328 (t0) REVERT: C 191 HIS cc_start: 0.8486 (m90) cc_final: 0.8116 (m-70) REVERT: C 197 ASP cc_start: 0.8951 (m-30) cc_final: 0.8610 (m-30) REVERT: C 242 GLN cc_start: 0.9031 (tt0) cc_final: 0.8754 (mt0) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.9573 time to fit residues: 44.7987 Evaluate side-chains 45 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.073847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052040 restraints weight = 32055.622| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.51 r_work: 0.2729 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4157 Z= 0.140 Angle : 0.517 6.383 5633 Z= 0.272 Chirality : 0.038 0.128 629 Planarity : 0.004 0.057 728 Dihedral : 3.992 18.079 554 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.22 % Allowed : 14.32 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.68 (0.39), residues: 504 helix: 1.77 (0.32), residues: 301 sheet: -0.20 (0.88), residues: 37 loop : 0.37 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 527 TYR 0.006 0.001 TYR C 265 PHE 0.022 0.001 PHE A 538 TRP 0.008 0.001 TRP A 417 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4156) covalent geometry : angle 0.51698 ( 5633) hydrogen bonds : bond 0.03599 ( 220) hydrogen bonds : angle 4.28906 ( 639) metal coordination : bond 0.00244 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 SER cc_start: 0.9522 (t) cc_final: 0.9241 (p) REVERT: A 570 ASP cc_start: 0.8796 (t0) cc_final: 0.8311 (t0) REVERT: C 191 HIS cc_start: 0.8496 (m90) cc_final: 0.8122 (m-70) REVERT: C 197 ASP cc_start: 0.8940 (m-30) cc_final: 0.8600 (m-30) REVERT: C 242 GLN cc_start: 0.9042 (tt0) cc_final: 0.8766 (mt0) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.9521 time to fit residues: 43.6989 Evaluate side-chains 43 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.074054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.052487 restraints weight = 31565.406| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.47 r_work: 0.2740 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4157 Z= 0.125 Angle : 0.510 6.327 5633 Z= 0.268 Chirality : 0.038 0.125 629 Planarity : 0.004 0.055 728 Dihedral : 3.950 17.854 554 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.22 % Allowed : 14.09 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.73 (0.39), residues: 504 helix: 1.85 (0.31), residues: 300 sheet: -0.17 (0.88), residues: 37 loop : 0.31 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 527 TYR 0.006 0.001 TYR C 265 PHE 0.022 0.001 PHE A 538 TRP 0.008 0.001 TRP A 417 HIS 0.003 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4156) covalent geometry : angle 0.50997 ( 5633) hydrogen bonds : bond 0.03496 ( 220) hydrogen bonds : angle 4.26457 ( 639) metal coordination : bond 0.00192 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.08 seconds wall clock time: 52 minutes 51.79 seconds (3171.79 seconds total)