Starting phenix.real_space_refine on Tue Feb 11 05:25:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5v_41934/02_2025/8u5v_41934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5v_41934/02_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_41934/02_2025/8u5v_41934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5v_41934/02_2025/8u5v_41934.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5v_41934/02_2025/8u5v_41934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5v_41934/02_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-5592/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: 3.00, per 1000 atoms: 0.68 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: 1.52 Conformation dependent library (CDL) restraints added in 582.4 milliseconds 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: 0.41 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: 1.24 Time building geometry restraints manager: 1.53 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: 0.080 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- 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= 0.514 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 *********************** 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 : 0.492 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: 0.9531 time to fit residues: 156.7022 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 : 0.537 ------------------------------------------------------------------------------- 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 = 0.096528 restraints weight = 7826.045| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.40 r_work: 0.3204 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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= 0.337 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 *********************** 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 : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.8882 (t80) cc_final: 0.8605 (t80) REVERT: A 159 GLN cc_start: 0.8872 (tt0) cc_final: 0.8648 (pt0) REVERT: A 193 TRP cc_start: 0.8696 (t60) cc_final: 0.8438 (t60) REVERT: A 212 LEU cc_start: 0.9171 (tp) cc_final: 0.8937 (tp) REVERT: A 299 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8220 (mp0) REVERT: A 388 ILE cc_start: 0.9296 (mt) cc_final: 0.9017 (mp) REVERT: A 394 LEU cc_start: 0.9193 (mt) cc_final: 0.8984 (mt) REVERT: A 469 PHE cc_start: 0.8830 (t80) cc_final: 0.8487 (t80) outliers start: 17 outliers final: 4 residues processed: 120 average time/residue: 0.9682 time to fit residues: 121.1807 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 : 0.447 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.7980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.128975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100178 restraints weight = 7900.724| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.42 r_work: 0.3263 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4504 Z= 0.201 Angle : 0.681 10.015 6125 Z= 0.328 Chirality : 0.043 0.169 740 Planarity : 0.004 0.032 729 Dihedral : 5.527 57.218 649 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: 2.54 (0.35), residues: 546 helix: 1.98 (0.23), residues: 452 sheet: None (None), residues: 0 loop : 0.36 (0.71), residues: 94 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 0.029 0.002 PHE A 221 TYR 0.022 0.002 TYR A 451 ARG 0.002 0.000 ARG A 295 *********************** 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 136 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7973 (mtm180) REVERT: A 76 PHE cc_start: 0.8827 (t80) cc_final: 0.8573 (t80) REVERT: A 146 ASP cc_start: 0.8859 (m-30) cc_final: 0.8536 (m-30) REVERT: A 159 GLN cc_start: 0.8847 (tt0) cc_final: 0.8594 (pt0) REVERT: A 164 GLU cc_start: 0.8987 (pm20) cc_final: 0.8715 (pm20) REVERT: A 193 TRP cc_start: 0.8567 (t60) cc_final: 0.8270 (t60) REVERT: A 234 ASP cc_start: 0.8739 (t0) cc_final: 0.8519 (t0) REVERT: A 235 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8266 (mtm-85) REVERT: A 295 ARG cc_start: 0.8591 (ttp80) cc_final: 0.7852 (ttt-90) REVERT: A 299 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8099 (mp0) REVERT: A 394 LEU cc_start: 0.9129 (mt) cc_final: 0.8917 (mt) REVERT: A 432 TRP cc_start: 0.8767 (t-100) cc_final: 0.8518 (t-100) REVERT: A 469 PHE cc_start: 0.8882 (t80) cc_final: 0.8524 (t80) REVERT: A 540 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8660 (mpp) REVERT: A 663 LEU cc_start: 0.9129 (mt) cc_final: 0.8869 (mp) outliers start: 15 outliers final: 4 residues processed: 129 average time/residue: 0.8943 time to fit residues: 121.0015 Evaluate side-chains 104 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 540 MET 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: 0.7980 chunk 52 optimal weight: 9.9990 chunk 33 optimal weight: 0.0020 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.128829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099536 restraints weight = 7997.583| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.47 r_work: 0.3256 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4504 Z= 0.235 Angle : 0.711 13.193 6125 Z= 0.335 Chirality : 0.044 0.216 740 Planarity : 0.004 0.042 729 Dihedral : 5.389 54.912 649 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.69 % Allowed : 19.83 % Favored : 77.48 % 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: 2.44 (0.35), residues: 546 helix: 1.99 (0.23), residues: 456 sheet: None (None), residues: 0 loop : -0.23 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.001 HIS A 505 PHE 0.029 0.002 PHE A 221 TYR 0.022 0.002 TYR A 451 ARG 0.003 0.000 ARG A 687 *********************** 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 121 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.7967 (mtm180) REVERT: A 159 GLN cc_start: 0.8819 (tt0) cc_final: 0.8533 (pt0) REVERT: A 193 TRP cc_start: 0.8569 (t60) cc_final: 0.8297 (t60) REVERT: A 235 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8279 (mtm-85) REVERT: A 295 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8275 (ttp80) REVERT: A 299 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8124 (mp0) REVERT: A 413 MET cc_start: 0.8298 (tpp) cc_final: 0.8061 (tpp) REVERT: A 432 TRP cc_start: 0.8799 (t-100) cc_final: 0.8554 (t-100) REVERT: A 466 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8921 (mt) REVERT: A 469 PHE cc_start: 0.8877 (t80) cc_final: 0.8510 (t80) REVERT: A 663 LEU cc_start: 0.9106 (mt) cc_final: 0.8818 (mp) outliers start: 13 outliers final: 8 residues processed: 115 average time/residue: 0.8156 time to fit residues: 98.7447 Evaluate side-chains 111 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 364 LEU Chi-restraints excluded: chain A residue 425 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096146 restraints weight = 8081.126| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.49 r_work: 0.3165 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4504 Z= 0.219 Angle : 0.704 10.686 6125 Z= 0.335 Chirality : 0.045 0.362 740 Planarity : 0.004 0.043 729 Dihedral : 5.308 55.356 649 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.72 % Allowed : 20.87 % Favored : 75.41 % 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: 2.56 (0.35), residues: 546 helix: 2.07 (0.23), residues: 456 sheet: None (None), residues: 0 loop : -0.21 (0.70), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.001 0.000 HIS A 658 PHE 0.028 0.002 PHE A 221 TYR 0.017 0.002 TYR A 451 ARG 0.002 0.000 ARG A 687 *********************** 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 128 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.8869 (m-30) cc_final: 0.8618 (m-30) REVERT: A 164 GLU cc_start: 0.9005 (pm20) cc_final: 0.8718 (pm20) REVERT: A 193 TRP cc_start: 0.8454 (t60) cc_final: 0.8227 (t60) REVERT: A 235 ARG cc_start: 0.8801 (mtm-85) cc_final: 0.8402 (mtm-85) REVERT: A 246 ASP cc_start: 0.8366 (m-30) cc_final: 0.8114 (m-30) REVERT: A 267 LYS cc_start: 0.8944 (mptp) cc_final: 0.8737 (mptm) REVERT: A 295 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8321 (ttp80) REVERT: A 299 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8152 (mp0) REVERT: A 469 PHE cc_start: 0.8865 (t80) cc_final: 0.8475 (t80) REVERT: A 491 ILE cc_start: 0.8265 (mt) cc_final: 0.7951 (mm) REVERT: A 663 LEU cc_start: 0.9108 (mt) cc_final: 0.8725 (mp) outliers start: 18 outliers final: 11 residues processed: 122 average time/residue: 0.9899 time to fit residues: 126.0533 Evaluate side-chains 112 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 364 LEU 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 676 CYS 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: 20.0000 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.126110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.095951 restraints weight = 7840.369| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.44 r_work: 0.3162 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4504 Z= 0.247 Angle : 0.720 10.024 6125 Z= 0.346 Chirality : 0.045 0.360 740 Planarity : 0.004 0.044 729 Dihedral : 5.052 54.283 647 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.72 % Allowed : 22.11 % Favored : 74.17 % 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: 2.57 (0.35), residues: 546 helix: 2.08 (0.23), residues: 456 sheet: None (None), residues: 0 loop : -0.21 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 460 HIS 0.002 0.001 HIS A 658 PHE 0.028 0.002 PHE A 221 TYR 0.024 0.002 TYR A 104 ARG 0.002 0.000 ARG A 235 *********************** 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 125 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8307 (m-80) cc_final: 0.7954 (m-80) REVERT: A 146 ASP cc_start: 0.8889 (m-30) cc_final: 0.8625 (m-30) REVERT: A 164 GLU cc_start: 0.9016 (pm20) cc_final: 0.8718 (pm20) REVERT: A 193 TRP cc_start: 0.8467 (t60) cc_final: 0.8239 (t60) REVERT: A 203 LYS cc_start: 0.8278 (mppt) cc_final: 0.7356 (mmmt) REVERT: A 235 ARG cc_start: 0.8713 (mtm-85) cc_final: 0.8356 (mtm-85) REVERT: A 246 ASP cc_start: 0.8344 (m-30) cc_final: 0.8086 (m-30) REVERT: A 267 LYS cc_start: 0.8955 (mptp) cc_final: 0.8741 (mptm) REVERT: A 295 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8366 (ttp80) REVERT: A 299 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8150 (mp0) REVERT: A 469 PHE cc_start: 0.8889 (t80) cc_final: 0.8471 (t80) REVERT: A 491 ILE cc_start: 0.8263 (mt) cc_final: 0.8002 (mm) REVERT: A 663 LEU cc_start: 0.9045 (mt) cc_final: 0.8711 (mp) outliers start: 18 outliers final: 12 residues processed: 117 average time/residue: 0.9492 time to fit residues: 116.2020 Evaluate side-chains 108 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 340 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 388 ILE 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 676 CYS 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: 4.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.0270 chunk 37 optimal weight: 8.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.128635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098940 restraints weight = 7936.389| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.43 r_work: 0.3218 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4530 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= 0.195 Angle : 0.684 10.318 6125 Z= 0.332 Chirality : 0.043 0.332 740 Planarity : 0.004 0.043 729 Dihedral : 4.961 55.845 647 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.72 % Allowed : 22.93 % 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: 2.61 (0.36), residues: 546 helix: 2.11 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -0.24 (0.72), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 460 HIS 0.002 0.001 HIS A 658 PHE 0.026 0.001 PHE A 221 TYR 0.020 0.002 TYR A 104 ARG 0.003 0.001 ARG A 235 *********************** 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 132 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8334 (mtm180) cc_final: 0.8086 (mtm180) REVERT: A 164 GLU cc_start: 0.8972 (pm20) cc_final: 0.8676 (pm20) REVERT: A 203 LYS cc_start: 0.8272 (mppt) cc_final: 0.7341 (mmmt) REVERT: A 235 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8352 (mtm-85) REVERT: A 299 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8158 (mp0) REVERT: A 451 TYR cc_start: 0.8219 (m-80) cc_final: 0.7947 (m-80) REVERT: A 469 PHE cc_start: 0.8877 (t80) cc_final: 0.8438 (t80) REVERT: A 491 ILE cc_start: 0.8164 (mt) cc_final: 0.7834 (mm) REVERT: A 534 ILE cc_start: 0.8716 (mt) cc_final: 0.8508 (tp) REVERT: A 658 HIS cc_start: 0.8309 (m-70) cc_final: 0.8094 (m90) REVERT: A 663 LEU cc_start: 0.9078 (mt) cc_final: 0.8784 (mp) outliers start: 18 outliers final: 10 residues processed: 124 average time/residue: 0.9824 time to fit residues: 127.1944 Evaluate side-chains 108 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 676 CYS 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: 0.9980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 443 GLN ** A 658 HIS ** 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 = 0.127403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097423 restraints weight = 7883.161| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.38 r_work: 0.3182 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4504 Z= 0.252 Angle : 0.761 14.036 6125 Z= 0.357 Chirality : 0.045 0.325 740 Planarity : 0.004 0.045 729 Dihedral : 5.162 54.413 647 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.27 % Allowed : 24.59 % Favored : 73.14 % 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: 2.62 (0.36), residues: 546 helix: 2.09 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -0.11 (0.75), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.002 0.001 HIS A 658 PHE 0.028 0.002 PHE A 221 TYR 0.017 0.002 TYR A 451 ARG 0.003 0.001 ARG A 295 *********************** 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 112 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8357 (mtm180) cc_final: 0.8096 (mtm180) REVERT: A 164 GLU cc_start: 0.9025 (pm20) cc_final: 0.8700 (pm20) REVERT: A 203 LYS cc_start: 0.8357 (mppt) cc_final: 0.7378 (mmmt) REVERT: A 222 MET cc_start: 0.8893 (mmm) cc_final: 0.8679 (mmm) REVERT: A 235 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.8345 (mtm-85) REVERT: A 299 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8183 (mp0) REVERT: A 381 ASN cc_start: 0.7777 (m-40) cc_final: 0.7301 (t0) REVERT: A 469 PHE cc_start: 0.8919 (t80) cc_final: 0.8493 (t80) REVERT: A 491 ILE cc_start: 0.8095 (mt) cc_final: 0.7824 (mm) REVERT: A 534 ILE cc_start: 0.8660 (mt) cc_final: 0.8445 (tp) REVERT: A 663 LEU cc_start: 0.9076 (mt) cc_final: 0.8786 (mp) outliers start: 11 outliers final: 9 residues processed: 110 average time/residue: 0.9810 time to fit residues: 112.7886 Evaluate side-chains 102 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 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 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 676 CYS 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: 0.9990 chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 50 optimal weight: 5.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.129489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100107 restraints weight = 7990.770| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.41 r_work: 0.3226 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4504 Z= 0.210 Angle : 0.762 10.125 6125 Z= 0.361 Chirality : 0.045 0.360 740 Planarity : 0.004 0.044 729 Dihedral : 5.101 52.427 647 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.27 % Allowed : 25.83 % Favored : 71.90 % 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: 2.57 (0.36), residues: 546 helix: 2.06 (0.24), residues: 460 sheet: None (None), residues: 0 loop : -0.21 (0.74), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 460 HIS 0.001 0.000 HIS A 658 PHE 0.025 0.002 PHE A 221 TYR 0.021 0.001 TYR A 451 ARG 0.004 0.001 ARG A 295 *********************** 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 113 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8310 (mtm180) cc_final: 0.8078 (mtm180) REVERT: A 146 ASP cc_start: 0.8866 (m-30) cc_final: 0.8515 (m-30) REVERT: A 164 GLU cc_start: 0.8984 (pm20) cc_final: 0.8673 (pm20) REVERT: A 203 LYS cc_start: 0.8384 (mppt) cc_final: 0.7324 (mmmt) REVERT: A 295 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8243 (ttp80) REVERT: A 299 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8181 (mp0) REVERT: A 381 ASN cc_start: 0.7746 (m-40) cc_final: 0.7321 (t0) REVERT: A 400 ILE cc_start: 0.9230 (tt) cc_final: 0.9005 (mm) REVERT: A 469 PHE cc_start: 0.8868 (t80) cc_final: 0.8395 (t80) REVERT: A 491 ILE cc_start: 0.7900 (mt) cc_final: 0.7590 (mm) REVERT: A 534 ILE cc_start: 0.8673 (mt) cc_final: 0.8461 (tp) REVERT: A 663 LEU cc_start: 0.9097 (mt) cc_final: 0.8879 (mp) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 1.0305 time to fit residues: 118.1556 Evaluate side-chains 108 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 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 696 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 0.0170 chunk 41 optimal weight: 6.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.130843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101245 restraints weight = 7879.575| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.47 r_work: 0.3249 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4504 Z= 0.213 Angle : 0.791 12.892 6125 Z= 0.371 Chirality : 0.045 0.352 740 Planarity : 0.004 0.044 729 Dihedral : 5.122 53.067 647 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.45 % Allowed : 27.27 % 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: 2.56 (0.36), residues: 546 helix: 2.08 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -0.34 (0.73), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.001 0.000 HIS A 412 PHE 0.023 0.001 PHE A 221 TYR 0.020 0.001 TYR A 451 ARG 0.007 0.001 ARG A 235 ********************** 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 116 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8287 (mtm180) cc_final: 0.8049 (mtm180) REVERT: A 76 PHE cc_start: 0.8594 (t80) cc_final: 0.8355 (t80) REVERT: A 146 ASP cc_start: 0.8911 (m-30) cc_final: 0.8544 (m-30) REVERT: A 164 GLU cc_start: 0.9030 (pm20) cc_final: 0.8677 (pm20) REVERT: A 203 LYS cc_start: 0.8335 (mppt) cc_final: 0.7293 (mmmt) REVERT: A 246 ASP cc_start: 0.8292 (m-30) cc_final: 0.8075 (m-30) REVERT: A 295 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8160 (ttp80) REVERT: A 299 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8175 (mp0) REVERT: A 381 ASN cc_start: 0.7701 (m-40) cc_final: 0.7284 (t0) REVERT: A 413 MET cc_start: 0.8193 (tpp) cc_final: 0.7874 (tmt) REVERT: A 469 PHE cc_start: 0.8885 (t80) cc_final: 0.8416 (t80) REVERT: A 534 ILE cc_start: 0.8624 (mt) cc_final: 0.8415 (tp) REVERT: A 540 MET cc_start: 0.8957 (mpp) cc_final: 0.8755 (mpm) REVERT: A 663 LEU cc_start: 0.9080 (mt) cc_final: 0.8745 (mp) REVERT: A 690 VAL cc_start: 0.8039 (t) cc_final: 0.7744 (p) outliers start: 7 outliers final: 7 residues processed: 115 average time/residue: 0.9110 time to fit residues: 109.6244 Evaluate side-chains 110 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 234 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: 6.9990 chunk 40 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.130339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100794 restraints weight = 7858.384| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.43 r_work: 0.3242 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4504 Z= 0.232 Angle : 0.789 9.776 6125 Z= 0.379 Chirality : 0.045 0.347 740 Planarity : 0.005 0.044 729 Dihedral : 5.151 53.799 647 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.45 % Allowed : 28.72 % Favored : 69.83 % 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: 2.00 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -0.23 (0.74), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 460 HIS 0.001 0.000 HIS A 412 PHE 0.025 0.002 PHE A 221 TYR 0.018 0.001 TYR A 451 ARG 0.004 0.001 ARG A 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.88 seconds wall clock time: 59 minutes 36.97 seconds (3576.97 seconds total)