Starting phenix.real_space_refine on Wed Mar 5 22:44:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3s_42952/03_2025/8v3s_42952.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3s_42952/03_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_42952/03_2025/8v3s_42952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3s_42952/03_2025/8v3s_42952.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3s_42952/03_2025/8v3s_42952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3s_42952/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.76, per 1000 atoms: 0.96 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: 0.93 Conformation dependent library (CDL) restraints added in 467.6 milliseconds 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: 0.44 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: 1.00 Time building geometry restraints manager: 1.12 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: 4.080 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.140 Find NCS groups from input model: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.290 ------------------------------------------------------------------------------- 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 : 0.398 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: 0.1799 time to fit residues: 15.4408 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 : 0.403 ------------------------------------------------------------------------------- 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 = 35)----------------| | 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 : 0.446 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: 0.1761 time to fit residues: 10.9247 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 : 0.468 ------------------------------------------------------------------------------- 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: 0.1980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.122647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110462 restraints weight = 5948.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113307 restraints weight = 3379.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115209 restraints weight = 2265.987| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4019 Z= 0.314 Angle : 0.637 11.108 5464 Z= 0.323 Chirality : 0.044 0.174 585 Planarity : 0.005 0.046 718 Dihedral : 5.034 51.189 557 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.98 % Allowed : 12.90 % Favored : 84.12 % 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: -0.11 (0.36), residues: 491 helix: 0.94 (0.41), residues: 143 sheet: 0.04 (0.55), residues: 77 loop : -0.63 (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 596 PHE 0.012 0.002 PHE A 268 TYR 0.027 0.002 TYR A 161 ARG 0.016 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 51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.443 Fit side-chains REVERT: A 150 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8221 (p) REVERT: A 557 GLN cc_start: 0.8607 (tp-100) cc_final: 0.8262 (tp-100) outliers start: 12 outliers final: 8 residues processed: 49 average time/residue: 0.1300 time to fit residues: 8.6291 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 : 0.440 ------------------------------------------------------------------------------- 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: 0.9990 chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 0.0070 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 13 optimal weight: 0.0870 chunk 30 optimal weight: 0.3980 chunk 6 optimal weight: 0.0670 chunk 33 optimal weight: 0.4980 chunk 1 optimal weight: 0.1980 chunk 36 optimal weight: 0.0980 overall best weight: 0.0914 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.125134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113047 restraints weight = 5995.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115963 restraints weight = 3337.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117778 restraints weight = 2206.283| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2667 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= 0.150 Angle : 0.546 10.577 5464 Z= 0.272 Chirality : 0.040 0.129 585 Planarity : 0.004 0.047 718 Dihedral : 4.741 53.321 557 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 16.13 % Favored : 81.14 % 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: 0.04 (0.37), residues: 491 helix: 1.15 (0.41), residues: 143 sheet: 0.23 (0.56), residues: 77 loop : -0.63 (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 0.004 0.000 ARG A 598 *********************** 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: 11 poor density : 37 time to evaluate : 0.422 Fit side-chains REVERT: A 191 TYR cc_start: 0.7546 (t80) cc_final: 0.7332 (t80) REVERT: A 459 MET cc_start: 0.8201 (mtt) cc_final: 0.7862 (mtp) REVERT: A 557 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8016 (tp-100) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 0.1470 time to fit residues: 9.1944 Evaluate side-chains 41 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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: 0.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.0470 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 overall best weight: 0.2976 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107835 restraints weight = 6246.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110620 restraints weight = 3608.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112553 restraints weight = 2452.703| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4019 Z= 0.296 Angle : 0.598 9.916 5464 Z= 0.302 Chirality : 0.042 0.130 585 Planarity : 0.005 0.045 718 Dihedral : 4.868 54.306 557 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.72 % Allowed : 14.64 % 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: -0.02 (0.36), residues: 491 helix: 1.00 (0.41), residues: 144 sheet: 0.48 (0.55), residues: 85 loop : -0.75 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.003 0.001 HIS A 511 PHE 0.023 0.002 PHE A 135 TYR 0.017 0.002 TYR A 161 ARG 0.005 0.001 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 51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.438 Fit side-chains REVERT: A 191 TYR cc_start: 0.7499 (t80) cc_final: 0.7253 (t80) REVERT: A 287 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7734 (mmtm) REVERT: A 459 MET cc_start: 0.8218 (mtt) cc_final: 0.7966 (mtt) REVERT: A 557 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8258 (tp-100) REVERT: A 593 MET cc_start: 0.8118 (tpp) cc_final: 0.7904 (tpp) outliers start: 15 outliers final: 13 residues processed: 50 average time/residue: 0.1488 time to fit residues: 9.7651 Evaluate side-chains 48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 578 ILE Chi-restraints excluded: chain A residue 583 HIS 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: 0.4980 chunk 16 optimal weight: 0.0980 chunk 33 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 18 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 overall best weight: 0.0956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.093852 restraints weight = 6425.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096521 restraints weight = 3733.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098613 restraints weight = 2581.401| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3139 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= 0.151 Angle : 0.535 9.322 5464 Z= 0.267 Chirality : 0.040 0.129 585 Planarity : 0.004 0.048 718 Dihedral : 4.638 53.791 557 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 0.17 (0.37), residues: 491 helix: 1.26 (0.41), residues: 144 sheet: 0.67 (0.56), residues: 85 loop : -0.73 (0.37), 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 336 PHE 0.010 0.001 PHE A 135 TYR 0.017 0.001 TYR A 161 ARG 0.003 0.000 ARG A 598 *********************** 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: 14 poor density : 38 time to evaluate : 0.452 Fit side-chains REVERT: A 104 GLN cc_start: 0.8374 (mt0) cc_final: 0.8113 (mt0) REVERT: A 191 TYR cc_start: 0.7781 (t80) cc_final: 0.7447 (t80) REVERT: A 440 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8069 (mtm180) REVERT: A 459 MET cc_start: 0.8478 (mtt) cc_final: 0.8198 (mtt) REVERT: A 593 MET cc_start: 0.8119 (tpp) cc_final: 0.7896 (tpp) REVERT: A 595 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8126 (mtmm) outliers start: 14 outliers final: 11 residues processed: 51 average time/residue: 0.1635 time to fit residues: 10.7289 Evaluate side-chains 47 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 309 VAL Chi-restraints excluded: chain A residue 321 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 31 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.1980 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.108471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.095080 restraints weight = 6386.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097782 restraints weight = 3764.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099798 restraints weight = 2576.531| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4019 Z= 0.214 Angle : 0.547 8.895 5464 Z= 0.274 Chirality : 0.041 0.129 585 Planarity : 0.004 0.048 718 Dihedral : 4.613 52.666 557 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.85 % Favored : 96.95 % Rotamer: Outliers : 4.22 % Allowed : 13.90 % Favored : 81.89 % 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: 0.21 (0.37), residues: 491 helix: 1.28 (0.41), residues: 144 sheet: 0.79 (0.56), residues: 85 loop : -0.73 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 57 HIS 0.003 0.001 HIS A 336 PHE 0.008 0.001 PHE A 135 TYR 0.015 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 53 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.416 Fit side-chains REVERT: A 314 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7359 (mm-40) REVERT: A 440 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8067 (mtm180) REVERT: A 459 MET cc_start: 0.8529 (mtt) cc_final: 0.8232 (mtt) REVERT: A 593 MET cc_start: 0.8100 (tpp) cc_final: 0.7858 (tpp) outliers start: 17 outliers final: 13 residues processed: 52 average time/residue: 0.1434 time to fit residues: 9.7344 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 : 0.408 ------------------------------------------------------------------------------- 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 321 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 chunk 35 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 14 optimal weight: 0.2980 overall best weight: 0.2376 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093365 restraints weight = 6405.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.096202 restraints weight = 3777.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098172 restraints weight = 2591.507| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4019 Z= 0.244 Angle : 0.569 8.619 5464 Z= 0.286 Chirality : 0.041 0.127 585 Planarity : 0.004 0.047 718 Dihedral : 4.651 51.227 557 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.65 % Favored : 97.15 % Rotamer: Outliers : 3.97 % Allowed : 14.39 % 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: 0.20 (0.36), residues: 491 helix: 1.35 (0.42), residues: 140 sheet: 0.87 (0.56), residues: 85 loop : -0.80 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 57 HIS 0.002 0.001 HIS A 596 PHE 0.010 0.001 PHE A 139 TYR 0.015 0.002 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 53 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.442 Fit side-chains REVERT: A 314 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7403 (mm-40) REVERT: A 440 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8160 (mtm180) REVERT: A 459 MET cc_start: 0.8498 (mtt) cc_final: 0.8265 (mtt) REVERT: A 595 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8307 (mtmm) outliers start: 16 outliers final: 13 residues processed: 52 average time/residue: 0.1646 time to fit residues: 10.9452 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 : 0.446 ------------------------------------------------------------------------------- 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 321 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.0060 chunk 39 optimal weight: 0.0670 chunk 40 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 overall best weight: 0.2112 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.091503 restraints weight = 6513.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094329 restraints weight = 3846.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096213 restraints weight = 2633.656| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4019 Z= 0.226 Angle : 0.568 8.284 5464 Z= 0.285 Chirality : 0.041 0.135 585 Planarity : 0.004 0.048 718 Dihedral : 4.587 48.714 557 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.44 % Favored : 97.35 % 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: 0.22 (0.36), residues: 491 helix: 1.43 (0.42), residues: 138 sheet: 0.83 (0.56), residues: 85 loop : -0.79 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 57 HIS 0.003 0.001 HIS A 336 PHE 0.010 0.001 PHE A 286 TYR 0.015 0.001 TYR A 161 ARG 0.006 0.000 ARG A 537 *********************** 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 54 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.421 Fit side-chains REVERT: A 130 MET cc_start: 0.6386 (tpt) cc_final: 0.6094 (tpt) REVERT: A 314 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7414 (mm-40) REVERT: A 440 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8155 (mtm180) REVERT: A 459 MET cc_start: 0.8501 (mtt) cc_final: 0.8272 (mtt) REVERT: A 595 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8275 (mtmm) outliers start: 17 outliers final: 14 residues processed: 52 average time/residue: 0.1535 time to fit residues: 10.4848 Evaluate side-chains 51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 160 SER 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 321 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 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.0020 chunk 33 optimal weight: 0.0970 chunk 17 optimal weight: 0.4980 chunk 45 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 29 optimal weight: 0.0000 chunk 27 optimal weight: 0.1980 overall best weight: 0.0568 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.109127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.095592 restraints weight = 6358.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098432 restraints weight = 3713.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100433 restraints weight = 2544.666| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3678 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= 0.148 Angle : 0.543 8.120 5464 Z= 0.269 Chirality : 0.039 0.135 585 Planarity : 0.004 0.050 718 Dihedral : 4.371 44.946 557 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.04 % Favored : 97.76 % Rotamer: Outliers : 3.23 % Allowed : 14.64 % 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: 0.41 (0.37), residues: 491 helix: 1.57 (0.42), residues: 138 sheet: 1.07 (0.57), residues: 85 loop : -0.70 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 57 HIS 0.003 0.001 HIS A 336 PHE 0.007 0.001 PHE A 109 TYR 0.015 0.001 TYR A 161 ARG 0.006 0.000 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 51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.474 Fit side-chains REVERT: A 130 MET cc_start: 0.6214 (tpt) cc_final: 0.6002 (tpt) REVERT: A 191 TYR cc_start: 0.7734 (t80) cc_final: 0.7307 (t80) REVERT: A 314 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7447 (mm-40) REVERT: A 440 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8105 (mtm180) REVERT: A 459 MET cc_start: 0.8526 (mtt) cc_final: 0.8240 (mtt) REVERT: A 593 MET cc_start: 0.8052 (tpp) cc_final: 0.7830 (tpp) REVERT: A 595 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8314 (mtmm) outliers start: 13 outliers final: 12 residues processed: 51 average time/residue: 0.1588 time to fit residues: 10.5812 Evaluate side-chains 51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 160 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 321 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: 0.8980 chunk 19 optimal weight: 0.0020 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.0070 chunk 23 optimal weight: 0.2980 chunk 47 optimal weight: 0.0270 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.1464 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.107639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.094390 restraints weight = 6320.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097174 restraints weight = 3713.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099130 restraints weight = 2541.571| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3737 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= 0.187 Angle : 0.553 7.707 5464 Z= 0.276 Chirality : 0.040 0.137 585 Planarity : 0.004 0.050 718 Dihedral : 4.329 42.758 557 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.65 % Favored : 97.15 % Rotamer: Outliers : 3.72 % Allowed : 14.89 % Favored : 81.39 % 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: 0.43 (0.37), residues: 491 helix: 1.55 (0.42), residues: 138 sheet: 1.16 (0.57), residues: 85 loop : -0.70 (0.37), 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 434 PHE 0.010 0.001 PHE A 286 TYR 0.015 0.001 TYR A 161 ARG 0.005 0.000 ARG A 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1872.44 seconds wall clock time: 33 minutes 2.43 seconds (1982.43 seconds total)