Starting phenix.real_space_refine on Tue Feb 11 03:33:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3s_42952/02_2025/8v3s_42952.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3s_42952/02_2025/8v3s_42952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v3s_42952/02_2025/8v3s_42952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3s_42952/02_2025/8v3s_42952.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3s_42952/02_2025/8v3s_42952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3s_42952/02_2025/8v3s_42952.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 21 5.16 5 C 2492 2.51 5 N 697 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3909 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3870 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 35, 'TRANS': 463} Chain breaks: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 122 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.42, per 1000 atoms: 1.13 Number of scatterers: 3909 At special positions: 0 Unit cell: (80.925, 73.455, 69.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 21 16.00 O 698 8.00 N 697 7.00 C 2492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 434 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 252 " 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 31.5% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 256 through 270 removed outlier: 3.865A pdb=" N PHE A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 323 through 340 Processing helix chain 'A' and resid 451 through 467 removed outlier: 4.362A pdb=" N TYR A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Proline residue: A 462 - end of helix Processing helix chain 'A' and resid 481 through 486 removed outlier: 3.844A pdb=" N TYR A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 removed outlier: 3.659A pdb=" N GLY A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 551 through 570 removed outlier: 3.976A pdb=" N ALA A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 585 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 5.232A pdb=" N THR A 112 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ARG A 118 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.733A pdb=" N TYR A 52 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN A 91 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 54 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 198 removed outlier: 7.153A pdb=" N VAL A 205 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 245 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 289 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 247 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 244 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL A 431 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE A 246 " --> pdb=" O VAL A 431 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU A 433 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER A 248 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N GLY A 435 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 220 removed outlier: 5.843A pdb=" N ASP A 219 " --> pdb=" O ARG A 238 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 408 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: 1.07 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 713 1.31 - 1.44: 1089 1.44 - 1.57: 2182 1.57 - 1.69: 4 1.69 - 1.82: 31 Bond restraints: 4019 Sorted by residual: bond pdb=" N GLU M1001 " pdb=" CA GLU M1001 " ideal model delta sigma weight residual 1.458 1.525 -0.067 1.90e-02 2.77e+03 1.23e+01 bond pdb=" CZ ARG A 276 " pdb=" NH2 ARG A 276 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.10e+00 bond pdb=" CA GLU M1001 " pdb=" C GLU M1001 " ideal model delta sigma weight residual 1.525 1.588 -0.063 2.10e-02 2.27e+03 9.04e+00 bond pdb=" CZ ARG A 250 " pdb=" NH2 ARG A 250 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.96e+00 bond pdb=" CZ ARG A 238 " pdb=" NH2 ARG A 238 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.40e+00 ... (remaining 4014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 3959 1.50 - 2.99: 1199 2.99 - 4.48: 242 4.48 - 5.98: 48 5.98 - 7.47: 16 Bond angle restraints: 5464 Sorted by residual: angle pdb=" N ILE A 578 " pdb=" CA ILE A 578 " pdb=" C ILE A 578 " ideal model delta sigma weight residual 110.62 116.35 -5.73 1.02e+00 9.61e-01 3.16e+01 angle pdb=" C SER A 539 " pdb=" N PRO A 540 " pdb=" CA PRO A 540 " ideal model delta sigma weight residual 119.66 115.66 4.00 7.20e-01 1.93e+00 3.09e+01 angle pdb=" C ALA A 545 " pdb=" CA ALA A 545 " pdb=" CB ALA A 545 " ideal model delta sigma weight residual 116.54 110.26 6.28 1.15e+00 7.56e-01 2.98e+01 angle pdb=" C SER A 548 " pdb=" CA SER A 548 " pdb=" CB SER A 548 " ideal model delta sigma weight residual 117.23 110.47 6.76 1.36e+00 5.41e-01 2.47e+01 angle pdb=" OE1 GLN A 475 " pdb=" CD GLN A 475 " pdb=" NE2 GLN A 475 " ideal model delta sigma weight residual 122.60 117.71 4.89 1.00e+00 1.00e+00 2.39e+01 ... (remaining 5459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2194 17.82 - 35.65: 145 35.65 - 53.47: 25 53.47 - 71.30: 5 71.30 - 89.12: 3 Dihedral angle restraints: 2372 sinusoidal: 904 harmonic: 1468 Sorted by residual: dihedral pdb=" CA TYR A 519 " pdb=" C TYR A 519 " pdb=" N ASN A 520 " pdb=" CA ASN A 520 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA HIS A 583 " pdb=" C HIS A 583 " pdb=" N SER A 584 " pdb=" CA SER A 584 " ideal model delta harmonic sigma weight residual 180.00 -161.31 -18.69 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ARG A 72 " pdb=" C ARG A 72 " pdb=" N SER A 73 " pdb=" CA SER A 73 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 375 0.067 - 0.133: 130 0.133 - 0.200: 60 0.200 - 0.266: 14 0.266 - 0.333: 6 Chirality restraints: 585 Sorted by residual: chirality pdb=" CA SER A 16 " pdb=" N SER A 16 " pdb=" C SER A 16 " pdb=" CB SER A 16 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA GLU M1001 " pdb=" N GLU M1001 " pdb=" C GLU M1001 " pdb=" CB GLU M1001 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA GLU M 3 " pdb=" N GLU M 3 " pdb=" C GLU M 3 " pdb=" CB GLU M 3 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 582 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 519 " 0.050 2.00e-02 2.50e+03 2.65e-02 1.40e+01 pdb=" CG TYR A 519 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 519 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 519 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 519 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 519 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 519 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 519 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 192 " 0.037 2.00e-02 2.50e+03 2.90e-02 1.26e+01 pdb=" CG HIS A 192 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A 192 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS A 192 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 192 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 192 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 335 " -0.039 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR A 335 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 335 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 335 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 335 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 335 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 335 " -0.046 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 5 2.56 - 3.15: 3042 3.15 - 3.73: 6284 3.73 - 4.32: 8769 4.32 - 4.90: 14492 Nonbonded interactions: 32592 Sorted by model distance: nonbonded pdb=" OE1 GLU A 255 " pdb="ZN ZN A 701 " model vdw 1.978 2.230 nonbonded pdb=" OE2 GLU A 255 " pdb="ZN ZN A 701 " model vdw 2.097 2.230 nonbonded pdb=" CD GLU A 255 " pdb="ZN ZN A 701 " model vdw 2.263 2.460 nonbonded pdb=" OG1 THR A 521 " pdb=" O SER A 548 " model vdw 2.480 3.040 nonbonded pdb=" O ASN A 458 " pdb=" OH TYR A 513 " model vdw 2.555 3.040 ... (remaining 32587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.750 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.970 Find NCS groups from input model: 0.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.011 0.067 4019 Z= 0.750 Angle : 1.522 7.475 5464 Z= 1.003 Chirality : 0.086 0.333 585 Planarity : 0.011 0.067 718 Dihedral : 12.860 89.124 1424 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.33), residues: 491 helix: -0.47 (0.35), residues: 143 sheet: -0.15 (0.58), residues: 72 loop : -1.05 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.008 TRP A 575 HIS 0.018 0.006 HIS A 436 PHE 0.036 0.006 PHE A 265 TYR 0.050 0.012 TYR A 519 ARG 0.016 0.002 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8260 (mt) cc_final: 0.8056 (mm) REVERT: A 52 TYR cc_start: 0.7967 (m-80) cc_final: 0.7673 (m-10) REVERT: A 69 ASN cc_start: 0.7676 (t0) cc_final: 0.7414 (t0) REVERT: A 307 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6802 (ttp-170) REVERT: A 521 THR cc_start: 0.8097 (t) cc_final: 0.7822 (m) REVERT: A 557 GLN cc_start: 0.7552 (tp-100) cc_final: 0.6999 (tp-100) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1920 time to fit residues: 16.3548 Evaluate side-chains 38 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.1980 chunk 37 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 23 optimal weight: 0.0770 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 overall best weight: 0.0894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120372 restraints weight = 5912.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123291 restraints weight = 3342.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125152 restraints weight = 2196.750| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4019 Z= 0.171 Angle : 0.603 12.169 5464 Z= 0.304 Chirality : 0.042 0.151 585 Planarity : 0.005 0.043 718 Dihedral : 4.917 49.288 557 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.74 % Allowed : 11.17 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.36), residues: 491 helix: 0.82 (0.40), residues: 143 sheet: 0.21 (0.58), residues: 72 loop : -0.71 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 57 HIS 0.004 0.001 HIS A 192 PHE 0.015 0.001 PHE A 265 TYR 0.018 0.002 TYR A 461 ARG 0.006 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.449 Fit side-chains REVERT: A 557 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7898 (tp-100) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.1756 time to fit residues: 10.8827 Evaluate side-chains 41 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 578 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 0.0970 chunk 9 optimal weight: 0.0970 chunk 46 optimal weight: 0.0970 chunk 28 optimal weight: 0.4980 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 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 = 0.3547 r_free = 0.3547 target = 0.123656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111483 restraints weight = 5939.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114380 restraints weight = 3348.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116285 restraints weight = 2225.196| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4019 Z= 0.288 Angle : 0.619 11.205 5464 Z= 0.313 Chirality : 0.044 0.187 585 Planarity : 0.005 0.046 718 Dihedral : 4.968 50.514 557 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.98 % Allowed : 12.66 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.36), residues: 491 helix: 0.98 (0.41), residues: 143 sheet: 0.06 (0.56), residues: 77 loop : -0.62 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 119 HIS 0.003 0.001 HIS A 192 PHE 0.012 0.002 PHE A 268 TYR 0.026 0.002 TYR A 161 ARG 0.008 0.001 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.445 Fit side-chains REVERT: A 150 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 557 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8217 (tp-100) REVERT: A 595 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8345 (mtmm) outliers start: 12 outliers final: 8 residues processed: 49 average time/residue: 0.1465 time to fit residues: 9.4997 Evaluate side-chains 40 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 578 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 30 optimal weight: 0.0980 chunk 6 optimal weight: 0.0870 chunk 33 optimal weight: 0.3980 chunk 1 optimal weight: 0.4980 chunk 36 optimal weight: 0.0980 overall best weight: 0.0934 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.125749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113716 restraints weight = 5985.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116619 restraints weight = 3345.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118595 restraints weight = 2211.810| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4019 Z= 0.147 Angle : 0.541 10.434 5464 Z= 0.269 Chirality : 0.040 0.129 585 Planarity : 0.004 0.047 718 Dihedral : 4.710 52.485 557 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.98 % Allowed : 15.38 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.37), residues: 491 helix: 1.24 (0.41), residues: 143 sheet: 0.24 (0.57), residues: 77 loop : -0.66 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 57 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.001 PHE A 286 TYR 0.018 0.001 TYR A 161 ARG 0.002 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.475 Fit side-chains REVERT: A 191 TYR cc_start: 0.7531 (t80) cc_final: 0.7309 (t80) REVERT: A 557 GLN cc_start: 0.8346 (tp-100) cc_final: 0.8001 (tp-100) outliers start: 12 outliers final: 7 residues processed: 47 average time/residue: 0.1508 time to fit residues: 9.3457 Evaluate side-chains 40 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 578 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 15 optimal weight: 0.0970 chunk 16 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 overall best weight: 0.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 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 = 0.3552 r_free = 0.3552 target = 0.124261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111966 restraints weight = 6251.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114796 restraints weight = 3629.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116697 restraints weight = 2471.733| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4019 Z= 0.231 Angle : 0.570 9.820 5464 Z= 0.286 Chirality : 0.041 0.129 585 Planarity : 0.004 0.046 718 Dihedral : 4.724 53.177 557 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.47 % Allowed : 13.65 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.36), residues: 491 helix: 1.08 (0.41), residues: 144 sheet: 0.50 (0.56), residues: 85 loop : -0.76 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 119 HIS 0.003 0.001 HIS A 323 PHE 0.025 0.002 PHE A 135 TYR 0.017 0.002 TYR A 161 ARG 0.004 0.000 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.467 Fit side-chains REVERT: A 191 TYR cc_start: 0.7526 (t80) cc_final: 0.7314 (t80) REVERT: A 287 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7686 (mmtm) REVERT: A 459 MET cc_start: 0.8218 (mtt) cc_final: 0.7886 (mtp) REVERT: A 557 GLN cc_start: 0.8540 (tp-100) cc_final: 0.8196 (tp-100) REVERT: A 593 MET cc_start: 0.8059 (tpp) cc_final: 0.7818 (tpp) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.1367 time to fit residues: 9.4904 Evaluate side-chains 46 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 578 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.092366 restraints weight = 6447.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095120 restraints weight = 3816.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.097117 restraints weight = 2634.621| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4019 Z= 0.308 Angle : 0.596 9.521 5464 Z= 0.301 Chirality : 0.042 0.131 585 Planarity : 0.005 0.046 718 Dihedral : 4.862 54.058 557 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.05 % Favored : 96.74 % Rotamer: Outliers : 4.22 % Allowed : 14.14 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.36), residues: 491 helix: 1.17 (0.41), residues: 138 sheet: 0.48 (0.55), residues: 90 loop : -0.94 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 57 HIS 0.003 0.001 HIS A 323 PHE 0.013 0.002 PHE A 135 TYR 0.017 0.002 TYR A 161 ARG 0.003 0.001 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.437 Fit side-chains REVERT: A 104 GLN cc_start: 0.8491 (mt0) cc_final: 0.8195 (mt0) REVERT: A 314 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7481 (mm-40) REVERT: A 440 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8071 (mtm180) REVERT: A 459 MET cc_start: 0.8528 (mtt) cc_final: 0.8278 (mtt) outliers start: 17 outliers final: 14 residues processed: 51 average time/residue: 0.1603 time to fit residues: 10.4224 Evaluate side-chains 46 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.1980 chunk 30 optimal weight: 0.2980 chunk 33 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 45 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 0.0870 overall best weight: 0.1356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.096022 restraints weight = 6376.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098898 restraints weight = 3712.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100936 restraints weight = 2534.303| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4019 Z= 0.172 Angle : 0.535 9.095 5464 Z= 0.269 Chirality : 0.040 0.127 585 Planarity : 0.004 0.047 718 Dihedral : 4.644 51.999 557 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.65 % Favored : 97.15 % Rotamer: Outliers : 3.47 % Allowed : 14.39 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.36), residues: 491 helix: 1.38 (0.42), residues: 138 sheet: 0.80 (0.56), residues: 85 loop : -0.88 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 57 HIS 0.003 0.001 HIS A 336 PHE 0.008 0.001 PHE A 54 TYR 0.016 0.001 TYR A 161 ARG 0.003 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.499 Fit side-chains REVERT: A 314 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7485 (mm-40) REVERT: A 459 MET cc_start: 0.8483 (mtt) cc_final: 0.8184 (mtt) REVERT: A 593 MET cc_start: 0.8142 (tpp) cc_final: 0.7920 (tpp) outliers start: 14 outliers final: 12 residues processed: 47 average time/residue: 0.1315 time to fit residues: 8.4140 Evaluate side-chains 45 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 0.0870 chunk 13 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 35 optimal weight: 0.4980 chunk 36 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 overall best weight: 0.1756 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.109601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.095934 restraints weight = 6340.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098827 restraints weight = 3722.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100686 restraints weight = 2551.305| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4019 Z= 0.202 Angle : 0.545 8.422 5464 Z= 0.273 Chirality : 0.040 0.132 585 Planarity : 0.004 0.046 718 Dihedral : 4.591 49.397 557 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.65 % Favored : 97.15 % Rotamer: Outliers : 3.72 % Allowed : 13.90 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.37), residues: 491 helix: 1.45 (0.42), residues: 138 sheet: 0.86 (0.56), residues: 85 loop : -0.85 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 57 HIS 0.002 0.001 HIS A 336 PHE 0.011 0.001 PHE A 286 TYR 0.015 0.001 TYR A 161 ARG 0.003 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.420 Fit side-chains REVERT: A 314 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7519 (mm-40) REVERT: A 459 MET cc_start: 0.8535 (mtt) cc_final: 0.8294 (mtt) outliers start: 15 outliers final: 12 residues processed: 47 average time/residue: 0.1277 time to fit residues: 8.2280 Evaluate side-chains 45 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 overall best weight: 0.2498 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.108391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.094630 restraints weight = 6376.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.097606 restraints weight = 3646.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099608 restraints weight = 2460.417| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4019 Z= 0.251 Angle : 0.565 8.308 5464 Z= 0.284 Chirality : 0.041 0.136 585 Planarity : 0.004 0.047 718 Dihedral : 4.620 47.267 557 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.65 % Favored : 97.15 % Rotamer: Outliers : 3.47 % Allowed : 13.65 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.37), residues: 491 helix: 1.33 (0.42), residues: 138 sheet: 0.93 (0.57), residues: 85 loop : -0.87 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 57 HIS 0.003 0.001 HIS A 336 PHE 0.010 0.001 PHE A 286 TYR 0.016 0.002 TYR A 161 ARG 0.003 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.496 Fit side-chains REVERT: A 130 MET cc_start: 0.6437 (tpt) cc_final: 0.6231 (tpt) REVERT: A 314 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7546 (mm-40) REVERT: A 440 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8168 (mtm180) REVERT: A 459 MET cc_start: 0.8534 (mtt) cc_final: 0.8282 (mtt) outliers start: 14 outliers final: 13 residues processed: 48 average time/residue: 0.1786 time to fit residues: 11.0726 Evaluate side-chains 46 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.0470 chunk 33 optimal weight: 0.0970 chunk 17 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 34 optimal weight: 0.0770 chunk 41 optimal weight: 0.1980 chunk 29 optimal weight: 0.0070 chunk 27 optimal weight: 0.0980 overall best weight: 0.0652 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.111025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097411 restraints weight = 6303.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100362 restraints weight = 3700.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102382 restraints weight = 2531.470| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4019 Z= 0.146 Angle : 0.538 8.018 5464 Z= 0.268 Chirality : 0.039 0.144 585 Planarity : 0.004 0.051 718 Dihedral : 4.368 42.886 557 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.83 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 14.64 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.37), residues: 491 helix: 1.38 (0.42), residues: 144 sheet: 1.12 (0.57), residues: 85 loop : -0.68 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 57 HIS 0.003 0.001 HIS A 434 PHE 0.009 0.001 PHE A 54 TYR 0.015 0.001 TYR A 161 ARG 0.011 0.001 ARG A 537 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.496 Fit side-chains REVERT: A 130 MET cc_start: 0.6250 (tpt) cc_final: 0.5986 (tpt) REVERT: A 191 TYR cc_start: 0.7723 (t80) cc_final: 0.7302 (t80) REVERT: A 314 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7460 (mm-40) REVERT: A 440 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8192 (mtm180) REVERT: A 459 MET cc_start: 0.8530 (mtt) cc_final: 0.8229 (mtt) REVERT: A 593 MET cc_start: 0.8059 (tpp) cc_final: 0.7824 (tpp) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1496 time to fit residues: 9.2826 Evaluate side-chains 46 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 583 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 0.0170 chunk 19 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 37 optimal weight: 0.0060 chunk 5 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 overall best weight: 0.0812 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.111245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.097837 restraints weight = 6248.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100737 restraints weight = 3685.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102581 restraints weight = 2520.583| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4019 Z= 0.152 Angle : 0.533 7.900 5464 Z= 0.265 Chirality : 0.039 0.136 585 Planarity : 0.004 0.051 718 Dihedral : 4.210 38.465 557 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.24 % Favored : 97.56 % Rotamer: Outliers : 2.73 % Allowed : 14.89 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.37), residues: 491 helix: 1.43 (0.42), residues: 144 sheet: 1.23 (0.58), residues: 85 loop : -0.62 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 57 HIS 0.002 0.001 HIS A 434 PHE 0.008 0.001 PHE A 54 TYR 0.013 0.001 TYR A 161 ARG 0.006 0.000 ARG A 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.65 seconds wall clock time: 32 minutes 36.79 seconds (1956.79 seconds total)