Starting phenix.real_space_refine on Wed Jun 4 21:58:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5v_41934/06_2025/8u5v_41934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5v_41934/06_2025/8u5v_41934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u5v_41934/06_2025/8u5v_41934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5v_41934/06_2025/8u5v_41934.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5v_41934/06_2025/8u5v_41934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5v_41934/06_2025/8u5v_41934.cif" } resolution = 2.77 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= -0.001 sd= 0.075 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2957 2.51 5 N 674 2.21 5 O 738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4397 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4359 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 535} Chain breaks: 4 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'IAC': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.59, per 1000 atoms: 0.82 Number of scatterers: 4397 At special positions: 0 Unit cell: (90.8642, 69.8103, 76.4589, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 738 8.00 N 674 7.00 C 2957 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 1.0 seconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1042 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.719A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 125 Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.539A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 196 removed outlier: 3.800A pdb=" N TYR A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 238 through 265 removed outlier: 4.252A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.280A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.671A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 474 Processing helix chain 'A' and resid 480 through 500 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 516 through 544 removed outlier: 3.564A pdb=" N GLN A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 679 Processing helix chain 'A' and resid 688 through 711 removed outlier: 5.763A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1086 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: 2.04 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 649 1.30 - 1.43: 1202 1.43 - 1.55: 2607 1.55 - 1.68: 1 1.68 - 1.81: 45 Bond restraints: 4504 Sorted by residual: bond pdb=" C PHE A 447 " pdb=" O PHE A 447 " ideal model delta sigma weight residual 1.237 1.168 0.069 1.19e-02 7.06e+03 3.35e+01 bond pdb=" C TYR A 689 " pdb=" O TYR A 689 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.17e-02 7.31e+03 1.49e+01 bond pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.433 1.366 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C LEU A 692 " pdb=" O LEU A 692 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.31e-02 5.83e+03 9.41e+00 bond pdb=" N VAL A 448 " pdb=" CA VAL A 448 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.18e-02 7.18e+03 8.32e+00 ... (remaining 4499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 5860 2.35 - 4.70: 232 4.70 - 7.05: 25 7.05 - 9.40: 6 9.40 - 11.75: 2 Bond angle restraints: 6125 Sorted by residual: angle pdb=" N THR A 457 " pdb=" CA THR A 457 " pdb=" C THR A 457 " ideal model delta sigma weight residual 111.36 103.41 7.95 1.09e+00 8.42e-01 5.32e+01 angle pdb=" N GLN A 693 " pdb=" CA GLN A 693 " pdb=" C GLN A 693 " ideal model delta sigma weight residual 111.36 103.46 7.90 1.09e+00 8.42e-01 5.26e+01 angle pdb=" CA TYR A 689 " pdb=" C TYR A 689 " pdb=" O TYR A 689 " ideal model delta sigma weight residual 120.55 114.61 5.94 1.06e+00 8.90e-01 3.14e+01 angle pdb=" C TYR A 451 " pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " ideal model delta sigma weight residual 110.85 119.85 -9.00 1.70e+00 3.46e-01 2.80e+01 angle pdb=" C TRP A 460 " pdb=" N THR A 461 " pdb=" CA THR A 461 " ideal model delta sigma weight residual 120.28 114.12 6.16 1.34e+00 5.57e-01 2.12e+01 ... (remaining 6120 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.79: 2423 14.79 - 29.57: 200 29.57 - 44.35: 30 44.35 - 59.13: 13 59.13 - 73.91: 3 Dihedral angle restraints: 2669 sinusoidal: 1056 harmonic: 1613 Sorted by residual: dihedral pdb=" C TYR A 451 " pdb=" N TYR A 451 " pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " ideal model delta harmonic sigma weight residual -122.60 -139.64 17.04 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" N TYR A 451 " pdb=" C TYR A 451 " pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " ideal model delta harmonic sigma weight residual 122.80 136.98 -14.18 0 2.50e+00 1.60e-01 3.22e+01 dihedral pdb=" CA THR A 196 " pdb=" C THR A 196 " pdb=" N GLN A 197 " pdb=" CA GLN A 197 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 2666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 705 0.118 - 0.237: 34 0.237 - 0.355: 0 0.355 - 0.473: 0 0.473 - 0.592: 1 Chirality restraints: 740 Sorted by residual: chirality pdb=" CA TYR A 451 " pdb=" N TYR A 451 " pdb=" C TYR A 451 " pdb=" CB TYR A 451 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CA PHE A 221 " pdb=" N PHE A 221 " pdb=" C PHE A 221 " pdb=" CB PHE A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA PHE A 695 " pdb=" N PHE A 695 " pdb=" C PHE A 695 " pdb=" CB PHE A 695 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 737 not shown) Planarity restraints: 729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " 0.087 2.00e-02 2.50e+03 4.45e-02 3.95e+01 pdb=" CG TYR A 320 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 221 " -0.038 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE A 221 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 221 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 221 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 221 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 221 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 221 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 457 " 0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C THR A 457 " -0.061 2.00e-02 2.50e+03 pdb=" O THR A 457 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR A 458 " 0.021 2.00e-02 2.50e+03 ... (remaining 726 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1866 2.92 - 3.42: 4944 3.42 - 3.91: 7927 3.91 - 4.41: 9244 4.41 - 4.90: 14735 Nonbonded interactions: 38716 Sorted by model distance: nonbonded pdb=" O TYR A 458 " pdb=" OG SER A 531 " model vdw 2.429 3.040 nonbonded pdb=" OH TYR A 359 " pdb=" OD2 ASP A 385 " model vdw 2.458 3.040 nonbonded pdb=" O VAL A 117 " pdb=" OG1 THR A 121 " model vdw 2.510 3.040 nonbonded pdb=" O VAL A 340 " pdb=" OG1 THR A 344 " model vdw 2.544 3.040 nonbonded pdb=" OD1 ASP A 99 " pdb=" OG SER A 101 " model vdw 2.547 3.040 ... (remaining 38711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 40.150 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.910 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:211.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 272.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.008 0.069 4504 Z= 0.392 Angle : 1.069 11.747 6125 Z= 0.649 Chirality : 0.059 0.592 740 Planarity : 0.008 0.047 729 Dihedral : 11.857 73.905 1627 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.24 % Allowed : 2.89 % Favored : 95.87 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.00 % 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: -0.23 (0.32), residues: 546 helix: 0.07 (0.22), residues: 452 sheet: None (None), residues: 0 loop : -0.51 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.007 TRP A 489 HIS 0.005 0.002 HIS A 658 PHE 0.061 0.006 PHE A 221 TYR 0.087 0.008 TYR A 320 ARG 0.005 0.001 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.17161 ( 368) hydrogen bonds : angle 7.03364 ( 1086) covalent geometry : bond 0.00802 ( 4504) covalent geometry : angle 1.06921 ( 6125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.7874 (mt0) cc_final: 0.7543 (mt0) REVERT: A 71 LYS cc_start: 0.7667 (mtpt) cc_final: 0.7208 (pptt) REVERT: A 76 PHE cc_start: 0.8903 (t80) cc_final: 0.8682 (t80) REVERT: A 159 GLN cc_start: 0.8590 (tt0) cc_final: 0.8179 (pt0) REVERT: A 193 TRP cc_start: 0.7977 (t60) cc_final: 0.7738 (t60) REVERT: A 212 LEU cc_start: 0.8971 (tp) cc_final: 0.8707 (tp) REVERT: A 234 ASP cc_start: 0.8428 (t0) cc_final: 0.8220 (t0) REVERT: A 347 MET cc_start: 0.9092 (tmm) cc_final: 0.8809 (tmm) REVERT: A 434 PHE cc_start: 0.7769 (m-80) cc_final: 0.7487 (m-80) REVERT: A 469 PHE cc_start: 0.8024 (t80) cc_final: 0.7770 (t80) outliers start: 6 outliers final: 2 residues processed: 157 average time/residue: 1.6471 time to fit residues: 271.2578 Evaluate side-chains 102 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 511 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096526 restraints weight = 7826.039| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.40 r_work: 0.3204 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4504 Z= 0.234 Angle : 0.730 7.360 6125 Z= 0.371 Chirality : 0.045 0.171 740 Planarity : 0.005 0.032 729 Dihedral : 7.261 109.085 651 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.51 % Allowed : 13.84 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.02 (0.35), residues: 546 helix: 1.61 (0.23), residues: 453 sheet: None (None), residues: 0 loop : 0.26 (0.68), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 396 HIS 0.003 0.001 HIS A 658 PHE 0.032 0.002 PHE A 221 TYR 0.027 0.003 TYR A 689 ARG 0.003 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.06214 ( 368) hydrogen bonds : angle 5.18487 ( 1086) covalent geometry : bond 0.00528 ( 4504) covalent geometry : angle 0.72990 ( 6125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.8885 (t80) cc_final: 0.8609 (t80) REVERT: A 159 GLN cc_start: 0.8883 (tt0) cc_final: 0.8655 (pt0) REVERT: A 193 TRP cc_start: 0.8723 (t60) cc_final: 0.8461 (t60) REVERT: A 212 LEU cc_start: 0.9171 (tp) cc_final: 0.8938 (tp) REVERT: A 299 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8214 (mp0) REVERT: A 388 ILE cc_start: 0.9300 (mt) cc_final: 0.9023 (mp) REVERT: A 394 LEU cc_start: 0.9191 (mt) cc_final: 0.8985 (mt) REVERT: A 469 PHE cc_start: 0.8826 (t80) cc_final: 0.8484 (t80) outliers start: 17 outliers final: 4 residues processed: 120 average time/residue: 1.0008 time to fit residues: 125.4846 Evaluate side-chains 100 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100776 restraints weight = 7897.761| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.43 r_work: 0.3278 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4504 Z= 0.151 Angle : 0.672 10.454 6125 Z= 0.325 Chirality : 0.042 0.159 740 Planarity : 0.004 0.032 729 Dihedral : 5.498 57.699 649 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.10 % Allowed : 16.94 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.36 (0.35), residues: 546 helix: 1.91 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -0.15 (0.72), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.000 HIS A 412 PHE 0.028 0.002 PHE A 221 TYR 0.023 0.002 TYR A 451 ARG 0.002 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.05373 ( 368) hydrogen bonds : angle 4.82933 ( 1086) covalent geometry : bond 0.00318 ( 4504) covalent geometry : angle 0.67212 ( 6125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8222 (mtm-85) cc_final: 0.7927 (mtm180) REVERT: A 76 PHE cc_start: 0.8817 (t80) cc_final: 0.8571 (t80) REVERT: A 96 SER cc_start: 0.8765 (m) cc_final: 0.8525 (p) REVERT: A 104 TYR cc_start: 0.8455 (m-80) cc_final: 0.8177 (m-80) REVERT: A 146 ASP cc_start: 0.8868 (m-30) cc_final: 0.8564 (m-30) REVERT: A 159 GLN cc_start: 0.8839 (tt0) cc_final: 0.8580 (pt0) REVERT: A 164 GLU cc_start: 0.8985 (pm20) cc_final: 0.8706 (pm20) REVERT: A 193 TRP cc_start: 0.8595 (t60) cc_final: 0.8295 (t60) REVERT: A 234 ASP cc_start: 0.8721 (t0) cc_final: 0.8518 (t0) REVERT: A 235 ARG cc_start: 0.8803 (mtm-85) cc_final: 0.8270 (mtm-85) REVERT: A 295 ARG cc_start: 0.8573 (ttp80) cc_final: 0.7835 (ttt-90) REVERT: A 299 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8084 (mp0) REVERT: A 394 LEU cc_start: 0.9106 (mt) cc_final: 0.8871 (mt) REVERT: A 469 PHE cc_start: 0.8870 (t80) cc_final: 0.8516 (t80) REVERT: A 663 LEU cc_start: 0.9109 (mt) cc_final: 0.8854 (mp) REVERT: A 692 LEU cc_start: 0.8619 (tp) cc_final: 0.7866 (tp) outliers start: 15 outliers final: 3 residues processed: 133 average time/residue: 0.8419 time to fit residues: 117.4426 Evaluate side-chains 109 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.123858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092990 restraints weight = 7944.056| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.44 r_work: 0.3108 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4504 Z= 0.213 Angle : 0.746 13.402 6125 Z= 0.351 Chirality : 0.046 0.250 740 Planarity : 0.004 0.043 729 Dihedral : 5.155 52.769 647 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.07 % Allowed : 20.04 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.31 (0.35), residues: 546 helix: 1.89 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -0.26 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.001 0.001 HIS A 310 PHE 0.030 0.002 PHE A 221 TYR 0.027 0.002 TYR A 689 ARG 0.002 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.05523 ( 368) hydrogen bonds : angle 4.85497 ( 1086) covalent geometry : bond 0.00479 ( 4504) covalent geometry : angle 0.74610 ( 6125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.8868 (tt0) cc_final: 0.8648 (pt0) REVERT: A 164 GLU cc_start: 0.9016 (pm20) cc_final: 0.8735 (pm20) REVERT: A 193 TRP cc_start: 0.8568 (t60) cc_final: 0.8299 (t60) REVERT: A 235 ARG cc_start: 0.8855 (mtm-85) cc_final: 0.8339 (mtm-85) REVERT: A 295 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8423 (ttp80) REVERT: A 299 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8192 (mp0) REVERT: A 413 MET cc_start: 0.8128 (tpp) cc_final: 0.7899 (tpp) REVERT: A 469 PHE cc_start: 0.8866 (t80) cc_final: 0.8475 (t80) REVERT: A 663 LEU cc_start: 0.9118 (mt) cc_final: 0.8836 (mp) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 0.9271 time to fit residues: 104.7895 Evaluate side-chains 101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096909 restraints weight = 8029.473| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.45 r_work: 0.3178 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4504 Z= 0.149 Angle : 0.685 11.024 6125 Z= 0.328 Chirality : 0.045 0.357 740 Planarity : 0.004 0.043 729 Dihedral : 5.089 57.122 647 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.31 % Allowed : 20.45 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.41 (0.35), residues: 546 helix: 1.97 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -0.29 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 679 HIS 0.001 0.000 HIS A 658 PHE 0.027 0.002 PHE A 221 TYR 0.019 0.001 TYR A 451 ARG 0.003 0.000 ARG A 687 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 368) hydrogen bonds : angle 4.71369 ( 1086) covalent geometry : bond 0.00319 ( 4504) covalent geometry : angle 0.68503 ( 6125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8426 (m-80) cc_final: 0.8159 (m-80) REVERT: A 164 GLU cc_start: 0.8998 (pm20) cc_final: 0.8720 (pm20) REVERT: A 193 TRP cc_start: 0.8428 (t60) cc_final: 0.8199 (t60) REVERT: A 235 ARG cc_start: 0.8807 (mtm-85) cc_final: 0.8421 (mtm-85) REVERT: A 267 LYS cc_start: 0.8926 (mptp) cc_final: 0.8726 (mptm) REVERT: A 295 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8334 (ttp80) REVERT: A 299 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8104 (mp0) REVERT: A 396 TRP cc_start: 0.8451 (t-100) cc_final: 0.7097 (t60) REVERT: A 413 MET cc_start: 0.8009 (tpp) cc_final: 0.7571 (tpp) REVERT: A 469 PHE cc_start: 0.8864 (t80) cc_final: 0.8445 (t80) REVERT: A 663 LEU cc_start: 0.9119 (mt) cc_final: 0.8735 (mp) REVERT: A 679 TRP cc_start: 0.7318 (t-100) cc_final: 0.7108 (t-100) outliers start: 16 outliers final: 9 residues processed: 117 average time/residue: 0.9537 time to fit residues: 116.5458 Evaluate side-chains 105 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 30.0000 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.0030 chunk 34 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 31 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.126502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096098 restraints weight = 7830.146| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.46 r_work: 0.3163 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4504 Z= 0.165 Angle : 0.728 10.455 6125 Z= 0.342 Chirality : 0.045 0.357 740 Planarity : 0.004 0.046 729 Dihedral : 5.035 54.461 647 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.89 % Allowed : 24.17 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.41 (0.35), residues: 546 helix: 1.97 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -0.32 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 432 HIS 0.003 0.001 HIS A 658 PHE 0.028 0.002 PHE A 221 TYR 0.022 0.002 TYR A 689 ARG 0.002 0.000 ARG A 687 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 368) hydrogen bonds : angle 4.71992 ( 1086) covalent geometry : bond 0.00369 ( 4504) covalent geometry : angle 0.72831 ( 6125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.9003 (pm20) cc_final: 0.8714 (pm20) REVERT: A 193 TRP cc_start: 0.8435 (t60) cc_final: 0.8234 (t60) REVERT: A 203 LYS cc_start: 0.8302 (mppt) cc_final: 0.7361 (mmmt) REVERT: A 235 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: A 242 GLU cc_start: 0.7805 (tt0) cc_final: 0.7595 (tt0) REVERT: A 295 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8361 (ttp80) REVERT: A 299 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8152 (mp0) REVERT: A 413 MET cc_start: 0.7964 (tpp) cc_final: 0.7568 (tpp) REVERT: A 469 PHE cc_start: 0.8890 (t80) cc_final: 0.8451 (t80) REVERT: A 663 LEU cc_start: 0.9069 (mt) cc_final: 0.8769 (mp) REVERT: A 691 GLU cc_start: 0.8717 (mp0) cc_final: 0.8506 (mp0) outliers start: 14 outliers final: 10 residues processed: 107 average time/residue: 0.9792 time to fit residues: 109.5752 Evaluate side-chains 104 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.127313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097571 restraints weight = 7937.523| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.40 r_work: 0.3193 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4504 Z= 0.148 Angle : 0.704 10.947 6125 Z= 0.333 Chirality : 0.045 0.377 740 Planarity : 0.004 0.047 729 Dihedral : 5.038 55.215 647 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.10 % Allowed : 23.55 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.41 (0.35), residues: 546 helix: 1.96 (0.23), residues: 461 sheet: None (None), residues: 0 loop : -0.34 (0.73), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 432 HIS 0.002 0.001 HIS A 658 PHE 0.027 0.002 PHE A 221 TYR 0.021 0.002 TYR A 689 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 368) hydrogen bonds : angle 4.68582 ( 1086) covalent geometry : bond 0.00321 ( 4504) covalent geometry : angle 0.70356 ( 6125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.8990 (pm20) cc_final: 0.8702 (pm20) REVERT: A 203 LYS cc_start: 0.8294 (mppt) cc_final: 0.7372 (mmmt) REVERT: A 235 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8211 (mtm-85) REVERT: A 299 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8170 (mp0) REVERT: A 396 TRP cc_start: 0.8520 (t-100) cc_final: 0.7204 (t60) REVERT: A 413 MET cc_start: 0.8033 (tpp) cc_final: 0.7645 (tpp) REVERT: A 451 TYR cc_start: 0.8246 (m-80) cc_final: 0.8019 (m-80) REVERT: A 469 PHE cc_start: 0.8873 (t80) cc_final: 0.8443 (t80) REVERT: A 534 ILE cc_start: 0.8704 (mt) cc_final: 0.8431 (mm) REVERT: A 663 LEU cc_start: 0.9099 (mt) cc_final: 0.8810 (mp) REVERT: A 691 GLU cc_start: 0.8731 (mp0) cc_final: 0.8464 (mp0) outliers start: 15 outliers final: 9 residues processed: 119 average time/residue: 0.9037 time to fit residues: 112.5054 Evaluate side-chains 108 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.0170 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.128774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099244 restraints weight = 7893.758| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.40 r_work: 0.3217 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4504 Z= 0.148 Angle : 0.751 11.068 6125 Z= 0.350 Chirality : 0.044 0.341 740 Planarity : 0.004 0.047 729 Dihedral : 4.964 55.039 647 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.31 % Allowed : 23.76 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.48 (0.36), residues: 546 helix: 2.02 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -0.40 (0.73), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 193 HIS 0.001 0.000 HIS A 658 PHE 0.026 0.002 PHE A 221 TYR 0.017 0.001 TYR A 689 ARG 0.004 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04795 ( 368) hydrogen bonds : angle 4.65374 ( 1086) covalent geometry : bond 0.00323 ( 4504) covalent geometry : angle 0.75055 ( 6125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8318 (mtm180) cc_final: 0.8063 (mtm180) REVERT: A 146 ASP cc_start: 0.8920 (m-30) cc_final: 0.8550 (m-30) REVERT: A 164 GLU cc_start: 0.9008 (pm20) cc_final: 0.8677 (pm20) REVERT: A 203 LYS cc_start: 0.8318 (mppt) cc_final: 0.7352 (mmmt) REVERT: A 246 ASP cc_start: 0.8322 (m-30) cc_final: 0.8077 (m-30) REVERT: A 267 LYS cc_start: 0.8923 (mptp) cc_final: 0.8695 (mptm) REVERT: A 299 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8166 (mp0) REVERT: A 381 ASN cc_start: 0.7773 (m-40) cc_final: 0.7304 (t0) REVERT: A 396 TRP cc_start: 0.8438 (t-100) cc_final: 0.7084 (t60) REVERT: A 413 MET cc_start: 0.8017 (tpp) cc_final: 0.7624 (tpp) REVERT: A 469 PHE cc_start: 0.8886 (t80) cc_final: 0.8435 (t80) REVERT: A 534 ILE cc_start: 0.8680 (mt) cc_final: 0.8450 (tp) REVERT: A 663 LEU cc_start: 0.9080 (mt) cc_final: 0.8848 (mp) REVERT: A 691 GLU cc_start: 0.8619 (mp0) cc_final: 0.8252 (mp0) outliers start: 16 outliers final: 8 residues processed: 123 average time/residue: 0.8936 time to fit residues: 115.3111 Evaluate side-chains 111 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.127907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097511 restraints weight = 8039.119| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.45 r_work: 0.3185 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4504 Z= 0.167 Angle : 0.751 10.531 6125 Z= 0.357 Chirality : 0.045 0.363 740 Planarity : 0.005 0.045 729 Dihedral : 5.197 53.433 647 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.10 % Allowed : 25.62 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.38 (0.36), residues: 546 helix: 1.94 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -0.34 (0.73), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 460 HIS 0.002 0.001 HIS A 505 PHE 0.027 0.001 PHE A 221 TYR 0.027 0.002 TYR A 451 ARG 0.006 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 368) hydrogen bonds : angle 4.69949 ( 1086) covalent geometry : bond 0.00373 ( 4504) covalent geometry : angle 0.75113 ( 6125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8347 (mtm180) cc_final: 0.8089 (mtm180) REVERT: A 164 GLU cc_start: 0.9038 (pm20) cc_final: 0.8713 (pm20) REVERT: A 203 LYS cc_start: 0.8405 (mppt) cc_final: 0.7337 (mmmt) REVERT: A 267 LYS cc_start: 0.8924 (mptp) cc_final: 0.8703 (mptm) REVERT: A 299 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8186 (mp0) REVERT: A 381 ASN cc_start: 0.7766 (m-40) cc_final: 0.7317 (t0) REVERT: A 396 TRP cc_start: 0.8480 (t-100) cc_final: 0.7138 (t60) REVERT: A 413 MET cc_start: 0.8029 (tpp) cc_final: 0.7742 (tpp) REVERT: A 469 PHE cc_start: 0.8901 (t80) cc_final: 0.8430 (t80) REVERT: A 534 ILE cc_start: 0.8690 (mt) cc_final: 0.8474 (tp) REVERT: A 663 LEU cc_start: 0.9074 (mt) cc_final: 0.8849 (mp) REVERT: A 691 GLU cc_start: 0.8629 (mp0) cc_final: 0.8294 (mp0) outliers start: 15 outliers final: 10 residues processed: 111 average time/residue: 0.9962 time to fit residues: 115.7513 Evaluate side-chains 115 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099036 restraints weight = 7899.657| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.47 r_work: 0.3212 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4504 Z= 0.159 Angle : 0.817 14.403 6125 Z= 0.381 Chirality : 0.046 0.361 740 Planarity : 0.005 0.048 729 Dihedral : 5.221 52.550 647 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.07 % Allowed : 27.27 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.30 (0.36), residues: 546 helix: 1.90 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -0.44 (0.70), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.001 0.001 HIS A 505 PHE 0.025 0.001 PHE A 221 TYR 0.029 0.002 TYR A 104 ARG 0.004 0.001 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04852 ( 368) hydrogen bonds : angle 4.68373 ( 1086) covalent geometry : bond 0.00349 ( 4504) covalent geometry : angle 0.81734 ( 6125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8319 (mtm180) cc_final: 0.8071 (mtm180) REVERT: A 146 ASP cc_start: 0.8923 (m-30) cc_final: 0.8655 (m-30) REVERT: A 164 GLU cc_start: 0.9018 (pm20) cc_final: 0.8688 (pm20) REVERT: A 203 LYS cc_start: 0.8349 (mppt) cc_final: 0.7297 (mmmt) REVERT: A 267 LYS cc_start: 0.8905 (mptp) cc_final: 0.8672 (mptm) REVERT: A 295 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8246 (ttp80) REVERT: A 299 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8183 (mp0) REVERT: A 381 ASN cc_start: 0.7743 (m-40) cc_final: 0.7303 (t0) REVERT: A 396 TRP cc_start: 0.8482 (t-100) cc_final: 0.7112 (t60) REVERT: A 413 MET cc_start: 0.7996 (tpp) cc_final: 0.7652 (tpp) REVERT: A 469 PHE cc_start: 0.8892 (t80) cc_final: 0.8415 (t80) REVERT: A 534 ILE cc_start: 0.8675 (mt) cc_final: 0.8418 (tp) REVERT: A 663 LEU cc_start: 0.9108 (mt) cc_final: 0.8867 (mp) REVERT: A 691 GLU cc_start: 0.8569 (mp0) cc_final: 0.8251 (mp0) outliers start: 10 outliers final: 8 residues processed: 108 average time/residue: 1.0214 time to fit residues: 115.3724 Evaluate side-chains 114 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.129342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099565 restraints weight = 7890.195| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.43 r_work: 0.3217 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4504 Z= 0.157 Angle : 0.793 13.727 6125 Z= 0.371 Chirality : 0.045 0.360 740 Planarity : 0.005 0.046 729 Dihedral : 5.218 52.022 647 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.07 % Allowed : 26.65 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.26 (0.36), residues: 546 helix: 1.87 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -0.51 (0.70), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.001 HIS A 412 PHE 0.024 0.001 PHE A 221 TYR 0.024 0.002 TYR A 451 ARG 0.006 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04847 ( 368) hydrogen bonds : angle 4.68343 ( 1086) covalent geometry : bond 0.00343 ( 4504) covalent geometry : angle 0.79270 ( 6125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.57 seconds wall clock time: 68 minutes 47.02 seconds (4127.02 seconds total)