Starting phenix.real_space_refine on Sat May 10 00:11:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5x_41935/05_2025/8u5x_41935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5x_41935/05_2025/8u5x_41935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u5x_41935/05_2025/8u5x_41935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5x_41935/05_2025/8u5x_41935.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5x_41935/05_2025/8u5x_41935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5x_41935/05_2025/8u5x_41935.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.072 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 2984 2.51 5 N 688 2.21 5 O 753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4453 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4440 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.35, per 1000 atoms: 0.75 Number of scatterers: 4453 At special positions: 0 Unit cell: (93.0804, 72.0265, 77.567, 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 753 8.00 N 688 7.00 C 2984 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: 1.28 Conformation dependent library (CDL) restraints added in 659.7 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1064 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 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: 3.961A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.007A 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 removed outlier: 3.622A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' 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 Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 196 removed outlier: 4.328A 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 251 removed outlier: 4.205A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 265 removed outlier: 3.561A 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: 4.308A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.609A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 439 through 474 removed outlier: 3.556A pdb=" N GLY A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 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 Processing helix chain 'A' and resid 655 through 683 removed outlier: 3.688A pdb=" N GLY A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 711 removed outlier: 5.726A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1101 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: 1.28 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1306 1.34 - 1.46: 833 1.46 - 1.57: 2377 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 4561 Sorted by residual: bond pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.433 1.364 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C IAC A 901 " pdb=" C1 IAC A 901 " ideal model delta sigma weight residual 1.414 1.366 0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C17 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.487 1.532 -0.045 2.00e-02 2.50e+03 4.95e+00 bond pdb=" CA TRP A 679 " pdb=" C TRP A 679 " ideal model delta sigma weight residual 1.524 1.497 0.028 1.28e-02 6.10e+03 4.73e+00 bond pdb=" CB VAL A 425 " pdb=" CG2 VAL A 425 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.63e+00 ... (remaining 4556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 6082 2.70 - 5.40: 109 5.40 - 8.10: 9 8.10 - 10.80: 0 10.80 - 13.50: 2 Bond angle restraints: 6202 Sorted by residual: angle pdb=" C17 IAC A 901 " pdb=" C7 IAC A 901 " pdb=" C8 IAC A 901 " ideal model delta sigma weight residual 127.34 113.84 13.50 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " pdb=" C17 IAC A 901 " ideal model delta sigma weight residual 126.92 138.72 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CA TRP A 679 " pdb=" CB TRP A 679 " pdb=" CG TRP A 679 " ideal model delta sigma weight residual 113.60 106.51 7.09 1.90e+00 2.77e-01 1.39e+01 angle pdb=" CA PHE A 221 " pdb=" CB PHE A 221 " pdb=" CG PHE A 221 " ideal model delta sigma weight residual 113.80 117.33 -3.53 1.00e+00 1.00e+00 1.25e+01 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 119.97 -6.07 1.80e+00 3.09e-01 1.14e+01 ... (remaining 6197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 2474 17.37 - 34.75: 155 34.75 - 52.12: 21 52.12 - 69.49: 8 69.49 - 86.86: 1 Dihedral angle restraints: 2659 sinusoidal: 1008 harmonic: 1651 Sorted by residual: dihedral pdb=" CA GLN A 654 " pdb=" C GLN A 654 " pdb=" N LEU A 655 " pdb=" CA LEU A 655 " ideal model delta harmonic sigma weight residual 180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA TYR A 516 " pdb=" C TYR A 516 " pdb=" N GLY A 517 " pdb=" CA GLY A 517 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA GLN A 409 " pdb=" C GLN A 409 " pdb=" N LEU A 410 " pdb=" CA LEU A 410 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 2656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 501 0.043 - 0.087: 189 0.087 - 0.130: 47 0.130 - 0.174: 7 0.174 - 0.217: 2 Chirality restraints: 746 Sorted by residual: 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 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB THR A 457 " pdb=" CA THR A 457 " pdb=" OG1 THR A 457 " pdb=" CG2 THR A 457 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE A 65 " pdb=" N ILE A 65 " pdb=" C ILE A 65 " pdb=" CB ILE A 65 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 743 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 221 " -0.030 2.00e-02 2.50e+03 2.34e-02 9.59e+00 pdb=" CG PHE A 221 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 221 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 221 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 221 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 221 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 221 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 708 " -0.030 2.00e-02 2.50e+03 2.10e-02 7.72e+00 pdb=" CG PHE A 708 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 708 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 708 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 708 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 708 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 708 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " 0.036 2.00e-02 2.50e+03 1.88e-02 7.09e+00 pdb=" CG TYR A 320 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " 0.014 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1959 2.92 - 3.42: 5094 3.42 - 3.91: 7920 3.91 - 4.41: 9447 4.41 - 4.90: 14808 Nonbonded interactions: 39228 Sorted by model distance: nonbonded pdb=" OH TYR A 359 " pdb=" OD2 ASP A 385 " model vdw 2.428 3.040 nonbonded pdb=" O ASN A 682 " pdb=" N GLU A 684 " model vdw 2.455 3.120 nonbonded pdb=" O VAL A 117 " pdb=" OG1 THR A 121 " model vdw 2.459 3.040 nonbonded pdb=" O VAL A 340 " pdb=" OG1 THR A 344 " model vdw 2.479 3.040 nonbonded pdb=" O ILE A 400 " pdb=" OG SER A 404 " model vdw 2.498 3.040 ... (remaining 39223 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 4561 Z= 0.329 Angle : 0.875 13.500 6202 Z= 0.471 Chirality : 0.048 0.217 746 Planarity : 0.007 0.055 747 Dihedral : 12.003 86.862 1595 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.61 % Allowed : 2.86 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.95 (0.31), residues: 565 helix: -0.48 (0.21), residues: 452 sheet: None (None), residues: 0 loop : -0.50 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 679 HIS 0.008 0.004 HIS A 310 PHE 0.053 0.004 PHE A 221 TYR 0.036 0.004 TYR A 320 ARG 0.003 0.001 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.15998 ( 374) hydrogen bonds : angle 7.00831 ( 1101) covalent geometry : bond 0.00792 ( 4561) covalent geometry : angle 0.87462 ( 6202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8207 (tt0) cc_final: 0.6527 (tp30) REVERT: A 71 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7047 (pptt) REVERT: A 216 GLN cc_start: 0.8219 (mt0) cc_final: 0.7952 (mt0) REVERT: A 347 MET cc_start: 0.8699 (tmm) cc_final: 0.8462 (tmm) REVERT: A 359 TYR cc_start: 0.8855 (t80) cc_final: 0.8083 (t80) outliers start: 3 outliers final: 2 residues processed: 138 average time/residue: 0.8881 time to fit residues: 128.3106 Evaluate side-chains 99 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 202 ASN A 412 HIS A 658 HIS A 672 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.132518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101405 restraints weight = 8313.657| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.57 r_work: 0.3338 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4561 Z= 0.190 Angle : 0.732 8.423 6202 Z= 0.367 Chirality : 0.044 0.189 746 Planarity : 0.005 0.040 747 Dihedral : 5.721 46.244 604 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.06 % Allowed : 13.67 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.48 (0.34), residues: 565 helix: 1.28 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -0.04 (0.59), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 432 HIS 0.006 0.002 HIS A 658 PHE 0.032 0.002 PHE A 221 TYR 0.013 0.002 TYR A 516 ARG 0.004 0.001 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.05423 ( 374) hydrogen bonds : angle 5.05619 ( 1101) covalent geometry : bond 0.00423 ( 4561) covalent geometry : angle 0.73198 ( 6202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7587 (tt0) cc_final: 0.5501 (tp30) REVERT: A 71 LYS cc_start: 0.7277 (mtpt) cc_final: 0.6839 (mmmt) REVERT: A 170 TYR cc_start: 0.8892 (m-80) cc_final: 0.8619 (m-80) REVERT: A 193 TRP cc_start: 0.9023 (t60) cc_final: 0.8707 (t60) REVERT: A 277 VAL cc_start: 0.9152 (t) cc_final: 0.8922 (p) REVERT: A 299 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8644 (mt-10) REVERT: A 347 MET cc_start: 0.8620 (tmm) cc_final: 0.8338 (tmm) REVERT: A 373 LYS cc_start: 0.9329 (mppt) cc_final: 0.8970 (mmpt) REVERT: A 406 LYS cc_start: 0.9221 (mmtt) cc_final: 0.8937 (mttp) REVERT: A 451 TYR cc_start: 0.7217 (m-10) cc_final: 0.6445 (m-10) REVERT: A 492 PRO cc_start: 0.8298 (Cg_exo) cc_final: 0.8004 (Cg_endo) outliers start: 15 outliers final: 4 residues processed: 118 average time/residue: 0.8259 time to fit residues: 102.4560 Evaluate side-chains 99 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 662 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.132197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.100625 restraints weight = 8258.302| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.60 r_work: 0.3342 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4561 Z= 0.185 Angle : 0.710 10.858 6202 Z= 0.353 Chirality : 0.043 0.168 746 Planarity : 0.005 0.038 747 Dihedral : 5.042 38.783 602 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.27 % Allowed : 17.35 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.91 (0.35), residues: 565 helix: 1.62 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -0.10 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 489 HIS 0.001 0.000 HIS A 658 PHE 0.030 0.002 PHE A 221 TYR 0.010 0.002 TYR A 451 ARG 0.005 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.05169 ( 374) hydrogen bonds : angle 4.86995 ( 1101) covalent geometry : bond 0.00415 ( 4561) covalent geometry : angle 0.71005 ( 6202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7008 (mtm-85) REVERT: A 71 LYS cc_start: 0.7201 (mtpt) cc_final: 0.6744 (mmmt) REVERT: A 130 ARG cc_start: 0.8555 (ptp90) cc_final: 0.7822 (ptp90) REVERT: A 159 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8455 (tp-100) REVERT: A 170 TYR cc_start: 0.8926 (m-80) cc_final: 0.8657 (m-80) REVERT: A 203 LYS cc_start: 0.8028 (mmpt) cc_final: 0.7664 (mtmm) REVERT: A 277 VAL cc_start: 0.9148 (t) cc_final: 0.8913 (p) REVERT: A 341 GLU cc_start: 0.8708 (mp0) cc_final: 0.8479 (pm20) REVERT: A 347 MET cc_start: 0.8649 (tmm) cc_final: 0.8369 (tmm) REVERT: A 406 LYS cc_start: 0.9107 (mmtt) cc_final: 0.8836 (mttp) outliers start: 16 outliers final: 3 residues processed: 109 average time/residue: 0.8957 time to fit residues: 102.2350 Evaluate side-chains 92 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 457 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN ** A 654 GLN ** 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 = 0.3947 r_free = 0.3947 target = 0.135047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.103858 restraints weight = 8309.650| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.65 r_work: 0.3388 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4561 Z= 0.147 Angle : 0.681 8.517 6202 Z= 0.337 Chirality : 0.042 0.158 746 Planarity : 0.005 0.037 747 Dihedral : 4.523 20.011 600 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.24 % Allowed : 17.55 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.13 (0.35), residues: 565 helix: 1.76 (0.24), residues: 460 sheet: None (None), residues: 0 loop : 0.03 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 679 HIS 0.001 0.000 HIS A 505 PHE 0.028 0.002 PHE A 221 TYR 0.022 0.002 TYR A 451 ARG 0.006 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 374) hydrogen bonds : angle 4.62706 ( 1101) covalent geometry : bond 0.00324 ( 4561) covalent geometry : angle 0.68102 ( 6202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7146 (mtm-85) REVERT: A 61 ARG cc_start: 0.8866 (mmm-85) cc_final: 0.8659 (mmm-85) REVERT: A 71 LYS cc_start: 0.7069 (mtpt) cc_final: 0.6659 (mmmt) REVERT: A 99 ASP cc_start: 0.8553 (t0) cc_final: 0.8067 (t70) REVERT: A 130 ARG cc_start: 0.8574 (ptp90) cc_final: 0.7835 (ptp90) REVERT: A 146 ASP cc_start: 0.8901 (m-30) cc_final: 0.8696 (m-30) REVERT: A 159 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8443 (tp-100) REVERT: A 193 TRP cc_start: 0.8984 (t60) cc_final: 0.8647 (t60) REVERT: A 234 ASP cc_start: 0.8879 (t0) cc_final: 0.8227 (t0) REVERT: A 236 LYS cc_start: 0.8718 (mttt) cc_final: 0.8310 (mptt) REVERT: A 277 VAL cc_start: 0.9136 (t) cc_final: 0.8906 (p) REVERT: A 299 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8565 (mt-10) REVERT: A 347 MET cc_start: 0.8629 (tmm) cc_final: 0.8368 (tmm) REVERT: A 406 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8408 (tppt) REVERT: A 459 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7902 (mt) outliers start: 11 outliers final: 4 residues processed: 115 average time/residue: 0.9353 time to fit residues: 112.4580 Evaluate side-chains 100 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.135899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.104566 restraints weight = 8541.551| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.75 r_work: 0.3397 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4561 Z= 0.146 Angle : 0.696 13.914 6202 Z= 0.338 Chirality : 0.042 0.187 746 Planarity : 0.005 0.037 747 Dihedral : 4.360 19.329 600 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.63 % Allowed : 21.02 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.18 (0.36), residues: 565 helix: 1.81 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -0.08 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 432 HIS 0.003 0.001 HIS A 505 PHE 0.028 0.002 PHE A 221 TYR 0.043 0.002 TYR A 451 ARG 0.005 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 374) hydrogen bonds : angle 4.56382 ( 1101) covalent geometry : bond 0.00326 ( 4561) covalent geometry : angle 0.69628 ( 6202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.6956 (mtpt) cc_final: 0.6579 (mmmt) REVERT: A 130 ARG cc_start: 0.8578 (ptp90) cc_final: 0.7804 (ptp90) REVERT: A 159 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8530 (tp-100) REVERT: A 193 TRP cc_start: 0.8935 (t60) cc_final: 0.8589 (t60) REVERT: A 236 LYS cc_start: 0.8663 (mttt) cc_final: 0.8265 (mptt) REVERT: A 277 VAL cc_start: 0.9113 (t) cc_final: 0.8870 (p) REVERT: A 295 ARG cc_start: 0.8596 (ttp80) cc_final: 0.8132 (mtm110) REVERT: A 299 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8527 (mt-10) REVERT: A 347 MET cc_start: 0.8694 (tmm) cc_final: 0.8426 (tmm) REVERT: A 406 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8551 (tppt) REVERT: A 429 MET cc_start: 0.7769 (tpt) cc_final: 0.7193 (tpt) REVERT: A 459 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7906 (mt) REVERT: A 711 PHE cc_start: 0.8326 (m-80) cc_final: 0.8108 (m-10) outliers start: 8 outliers final: 4 residues processed: 106 average time/residue: 0.9661 time to fit residues: 106.9699 Evaluate side-chains 96 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** 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 = 0.3951 r_free = 0.3951 target = 0.135148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.103879 restraints weight = 8462.229| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.71 r_work: 0.3364 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4561 Z= 0.159 Angle : 0.713 11.254 6202 Z= 0.344 Chirality : 0.043 0.180 746 Planarity : 0.005 0.039 747 Dihedral : 4.291 19.019 600 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.86 % Allowed : 20.41 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.20 (0.36), residues: 565 helix: 1.76 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.23 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 679 HIS 0.002 0.001 HIS A 505 PHE 0.029 0.002 PHE A 221 TYR 0.050 0.002 TYR A 451 ARG 0.006 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 374) hydrogen bonds : angle 4.59738 ( 1101) covalent geometry : bond 0.00366 ( 4561) covalent geometry : angle 0.71321 ( 6202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7192 (mtm-85) REVERT: A 71 LYS cc_start: 0.6993 (mtpt) cc_final: 0.6593 (mmmt) REVERT: A 99 ASP cc_start: 0.8568 (t0) cc_final: 0.8122 (t70) REVERT: A 130 ARG cc_start: 0.8595 (ptp90) cc_final: 0.7812 (ptp90) REVERT: A 159 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8554 (tp-100) REVERT: A 193 TRP cc_start: 0.8902 (t60) cc_final: 0.8597 (t60) REVERT: A 234 ASP cc_start: 0.8891 (t0) cc_final: 0.8295 (t0) REVERT: A 236 LYS cc_start: 0.8669 (mttt) cc_final: 0.8270 (mptt) REVERT: A 246 ASP cc_start: 0.7907 (m-30) cc_final: 0.7691 (m-30) REVERT: A 277 VAL cc_start: 0.9118 (t) cc_final: 0.8872 (p) REVERT: A 299 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8545 (mt-10) REVERT: A 302 ASP cc_start: 0.8353 (t0) cc_final: 0.7943 (t0) REVERT: A 347 MET cc_start: 0.8680 (tmm) cc_final: 0.8421 (tmm) REVERT: A 406 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8524 (tppt) REVERT: A 459 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7982 (mt) REVERT: A 516 TYR cc_start: 0.8026 (m-80) cc_final: 0.7260 (t80) REVERT: A 665 LEU cc_start: 0.9327 (mt) cc_final: 0.9006 (pp) outliers start: 14 outliers final: 5 residues processed: 114 average time/residue: 0.9357 time to fit residues: 111.5504 Evaluate side-chains 96 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** 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 = 0.3965 r_free = 0.3965 target = 0.136243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105473 restraints weight = 8457.167| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.73 r_work: 0.3371 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4561 Z= 0.152 Angle : 0.737 12.772 6202 Z= 0.355 Chirality : 0.046 0.268 746 Planarity : 0.005 0.041 747 Dihedral : 4.312 18.806 600 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.06 % Allowed : 21.84 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.19 (0.36), residues: 565 helix: 1.73 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.37 (0.68), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 679 HIS 0.002 0.001 HIS A 505 PHE 0.028 0.001 PHE A 221 TYR 0.013 0.001 TYR A 451 ARG 0.006 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 374) hydrogen bonds : angle 4.57272 ( 1101) covalent geometry : bond 0.00346 ( 4561) covalent geometry : angle 0.73712 ( 6202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7037 (mtm-85) REVERT: A 71 LYS cc_start: 0.6950 (mtpt) cc_final: 0.6556 (mmmt) REVERT: A 130 ARG cc_start: 0.8600 (ptp90) cc_final: 0.7865 (ptp90) REVERT: A 193 TRP cc_start: 0.8881 (t60) cc_final: 0.8575 (t60) REVERT: A 236 LYS cc_start: 0.8622 (mttt) cc_final: 0.8205 (mptt) REVERT: A 277 VAL cc_start: 0.9094 (t) cc_final: 0.8857 (p) REVERT: A 295 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8029 (mtm110) REVERT: A 299 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8571 (mt-10) REVERT: A 347 MET cc_start: 0.8673 (tmm) cc_final: 0.8401 (tmm) REVERT: A 430 MET cc_start: 0.8497 (mtt) cc_final: 0.8050 (mpt) REVERT: A 459 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 516 TYR cc_start: 0.7963 (m-80) cc_final: 0.7113 (t80) REVERT: A 542 MET cc_start: 0.7313 (tmm) cc_final: 0.6842 (tpt) REVERT: A 665 LEU cc_start: 0.9281 (mt) cc_final: 0.9030 (pp) outliers start: 15 outliers final: 5 residues processed: 101 average time/residue: 0.9521 time to fit residues: 100.5722 Evaluate side-chains 96 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 532 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 3 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.137461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106244 restraints weight = 8268.559| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.72 r_work: 0.3416 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4561 Z= 0.145 Angle : 0.724 13.875 6202 Z= 0.348 Chirality : 0.044 0.271 746 Planarity : 0.005 0.041 747 Dihedral : 4.229 18.757 600 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.63 % Allowed : 24.08 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.29 (0.36), residues: 565 helix: 1.81 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.36 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 679 HIS 0.002 0.001 HIS A 505 PHE 0.027 0.002 PHE A 221 TYR 0.016 0.001 TYR A 451 ARG 0.006 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 374) hydrogen bonds : angle 4.52297 ( 1101) covalent geometry : bond 0.00331 ( 4561) covalent geometry : angle 0.72368 ( 6202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9186 (tp) cc_final: 0.8929 (mm) REVERT: A 71 LYS cc_start: 0.6985 (mtpt) cc_final: 0.6574 (mmmt) REVERT: A 99 ASP cc_start: 0.8576 (t0) cc_final: 0.8169 (t70) REVERT: A 130 ARG cc_start: 0.8621 (ptp90) cc_final: 0.7903 (ptp90) REVERT: A 193 TRP cc_start: 0.8864 (t60) cc_final: 0.8601 (t60) REVERT: A 234 ASP cc_start: 0.8828 (t0) cc_final: 0.8203 (t0) REVERT: A 236 LYS cc_start: 0.8624 (mttt) cc_final: 0.8235 (mptt) REVERT: A 246 ASP cc_start: 0.7929 (m-30) cc_final: 0.7699 (m-30) REVERT: A 277 VAL cc_start: 0.9108 (t) cc_final: 0.8881 (p) REVERT: A 295 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8122 (mtm110) REVERT: A 302 ASP cc_start: 0.8344 (t0) cc_final: 0.7927 (t0) REVERT: A 347 MET cc_start: 0.8645 (tmm) cc_final: 0.8371 (tmm) REVERT: A 385 ASP cc_start: 0.8275 (m-30) cc_final: 0.8071 (m-30) REVERT: A 429 MET cc_start: 0.8006 (tpt) cc_final: 0.7764 (tpt) REVERT: A 459 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8076 (mt) REVERT: A 511 ASP cc_start: 0.6664 (t0) cc_final: 0.6364 (t0) REVERT: A 516 TYR cc_start: 0.7806 (m-80) cc_final: 0.6987 (t80) REVERT: A 542 MET cc_start: 0.7483 (tmm) cc_final: 0.7030 (tpt) outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.8957 time to fit residues: 97.5928 Evaluate side-chains 101 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 532 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 17 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.136042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104732 restraints weight = 8311.138| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.72 r_work: 0.3377 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4561 Z= 0.164 Angle : 0.754 13.757 6202 Z= 0.362 Chirality : 0.047 0.295 746 Planarity : 0.005 0.041 747 Dihedral : 4.238 18.984 600 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.04 % Allowed : 24.08 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.23 (0.36), residues: 565 helix: 1.79 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.24 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 679 HIS 0.001 0.000 HIS A 505 PHE 0.029 0.002 PHE A 221 TYR 0.018 0.002 TYR A 689 ARG 0.007 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 374) hydrogen bonds : angle 4.60293 ( 1101) covalent geometry : bond 0.00385 ( 4561) covalent geometry : angle 0.75432 ( 6202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.6955 (mtpt) cc_final: 0.6552 (mmmt) REVERT: A 99 ASP cc_start: 0.8548 (t0) cc_final: 0.8099 (t70) REVERT: A 130 ARG cc_start: 0.8638 (ptp90) cc_final: 0.7912 (ptp90) REVERT: A 193 TRP cc_start: 0.8835 (t60) cc_final: 0.8624 (t60) REVERT: A 203 LYS cc_start: 0.7973 (mmpt) cc_final: 0.7589 (mtmm) REVERT: A 234 ASP cc_start: 0.8839 (t0) cc_final: 0.8235 (t0) REVERT: A 236 LYS cc_start: 0.8637 (mttt) cc_final: 0.8246 (mptt) REVERT: A 246 ASP cc_start: 0.7924 (m-30) cc_final: 0.7695 (m-30) REVERT: A 277 VAL cc_start: 0.9122 (t) cc_final: 0.8889 (p) REVERT: A 295 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8155 (mtm110) REVERT: A 302 ASP cc_start: 0.8361 (t0) cc_final: 0.7890 (t0) REVERT: A 347 MET cc_start: 0.8669 (tmm) cc_final: 0.8410 (tmm) REVERT: A 385 ASP cc_start: 0.8361 (m-30) cc_final: 0.8154 (m-30) REVERT: A 429 MET cc_start: 0.8030 (tpt) cc_final: 0.7796 (tpt) REVERT: A 459 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8051 (mt) REVERT: A 516 TYR cc_start: 0.7883 (m-80) cc_final: 0.6986 (t80) REVERT: A 542 MET cc_start: 0.7488 (tmm) cc_final: 0.7219 (tmm) outliers start: 10 outliers final: 3 residues processed: 93 average time/residue: 0.9631 time to fit residues: 93.9849 Evaluate side-chains 94 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 532 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.138309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.107441 restraints weight = 8448.098| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.74 r_work: 0.3435 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4561 Z= 0.148 Angle : 0.778 15.856 6202 Z= 0.366 Chirality : 0.048 0.312 746 Planarity : 0.005 0.041 747 Dihedral : 4.216 18.505 600 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.02 % Allowed : 25.31 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.15 (0.36), residues: 565 helix: 1.77 (0.24), residues: 469 sheet: None (None), residues: 0 loop : -0.15 (0.68), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 679 HIS 0.001 0.000 HIS A 505 PHE 0.027 0.001 PHE A 221 TYR 0.017 0.001 TYR A 689 ARG 0.007 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 374) hydrogen bonds : angle 4.61564 ( 1101) covalent geometry : bond 0.00341 ( 4561) covalent geometry : angle 0.77809 ( 6202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7102 (mtm-85) REVERT: A 54 LEU cc_start: 0.9165 (tp) cc_final: 0.8928 (mm) REVERT: A 71 LYS cc_start: 0.6975 (mtpt) cc_final: 0.6526 (mmmt) REVERT: A 99 ASP cc_start: 0.8553 (t0) cc_final: 0.8209 (t70) REVERT: A 130 ARG cc_start: 0.8642 (ptp90) cc_final: 0.7919 (ptp90) REVERT: A 193 TRP cc_start: 0.8801 (t60) cc_final: 0.8542 (t60) REVERT: A 194 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8408 (ttpp) REVERT: A 234 ASP cc_start: 0.8797 (t0) cc_final: 0.8168 (t0) REVERT: A 236 LYS cc_start: 0.8579 (mttt) cc_final: 0.8208 (mptt) REVERT: A 246 ASP cc_start: 0.7926 (m-30) cc_final: 0.7683 (m-30) REVERT: A 277 VAL cc_start: 0.9086 (t) cc_final: 0.8865 (p) REVERT: A 295 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8029 (mtm110) REVERT: A 299 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8586 (mp0) REVERT: A 302 ASP cc_start: 0.8382 (t0) cc_final: 0.7923 (t0) REVERT: A 347 MET cc_start: 0.8662 (tmm) cc_final: 0.8379 (tmm) REVERT: A 385 ASP cc_start: 0.8283 (m-30) cc_final: 0.8071 (m-30) REVERT: A 396 TRP cc_start: 0.8366 (t-100) cc_final: 0.8025 (t-100) REVERT: A 459 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8049 (mt) REVERT: A 516 TYR cc_start: 0.7735 (m-80) cc_final: 0.7193 (t80) REVERT: A 521 MET cc_start: 0.7475 (mmt) cc_final: 0.7057 (mmt) REVERT: A 542 MET cc_start: 0.7482 (tmm) cc_final: 0.7117 (tpt) outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.9363 time to fit residues: 91.2714 Evaluate side-chains 94 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 532 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.138199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107645 restraints weight = 8371.882| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.73 r_work: 0.3408 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4561 Z= 0.156 Angle : 0.766 14.032 6202 Z= 0.366 Chirality : 0.047 0.273 746 Planarity : 0.005 0.041 747 Dihedral : 4.210 18.598 600 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.82 % Allowed : 25.51 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.18 (0.36), residues: 565 helix: 1.78 (0.24), residues: 469 sheet: None (None), residues: 0 loop : -0.10 (0.69), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 679 HIS 0.005 0.001 HIS A 658 PHE 0.028 0.002 PHE A 221 TYR 0.025 0.002 TYR A 689 ARG 0.007 0.001 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 374) hydrogen bonds : angle 4.56746 ( 1101) covalent geometry : bond 0.00359 ( 4561) covalent geometry : angle 0.76626 ( 6202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3191.31 seconds wall clock time: 55 minutes 56.09 seconds (3356.09 seconds total)