Starting phenix.real_space_refine on Wed Mar 5 19:10:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlc_32581/03_2025/7wlc_32581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlc_32581/03_2025/7wlc_32581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wlc_32581/03_2025/7wlc_32581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlc_32581/03_2025/7wlc_32581.map" model { file = "/net/cci-nas-00/data/ceres_data/7wlc_32581/03_2025/7wlc_32581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlc_32581/03_2025/7wlc_32581.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2094 2.51 5 N 563 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 3307 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.67, per 1000 atoms: 1.11 Number of scatterers: 3307 At special positions: 0 Unit cell: (53.04, 80.08, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 636 8.00 N 563 7.00 C 2094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 453.3 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 8.8% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.781A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 removed outlier: 3.657A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 389' Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.535A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.569A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.730A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.730A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 391 through 392 removed outlier: 3.634A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.789A pdb=" N GLU H 10 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA H 118 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.625A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23 100 hydrogen bonds defined for protein. 237 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: 0.81 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1071 1.34 - 1.47: 889 1.47 - 1.59: 1416 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 3392 Sorted by residual: bond pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB ASN E 448 " pdb=" CG ASN E 448 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta sigma weight residual 1.444 1.454 -0.010 9.60e-03 1.09e+04 9.95e-01 bond pdb=" C ASN E 331 " pdb=" N ILE E 332 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 9.85e-01 bond pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.82e-01 ... (remaining 3387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4508 1.92 - 3.83: 86 3.83 - 5.75: 13 5.75 - 7.67: 5 7.67 - 9.59: 2 Bond angle restraints: 4614 Sorted by residual: angle pdb=" C ASN E 331 " pdb=" N ILE E 332 " pdb=" CA ILE E 332 " ideal model delta sigma weight residual 121.70 128.16 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA MET H 81 " pdb=" CB MET H 81 " pdb=" CG MET H 81 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 111.30 119.20 -7.90 2.30e+00 1.89e-01 1.18e+01 angle pdb=" CB MET H 81 " pdb=" CG MET H 81 " pdb=" SD MET H 81 " ideal model delta sigma weight residual 112.70 103.11 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA TRP H 111 " pdb=" CB TRP H 111 " pdb=" CG TRP H 111 " ideal model delta sigma weight residual 113.60 119.66 -6.06 1.90e+00 2.77e-01 1.02e+01 ... (remaining 4609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 1779 15.37 - 30.74: 175 30.74 - 46.11: 29 46.11 - 61.48: 13 61.48 - 76.85: 8 Dihedral angle restraints: 2004 sinusoidal: 768 harmonic: 1236 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 28.64 64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual 93.00 34.26 58.74 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CA MET H 81 " pdb=" C MET H 81 " pdb=" N GLU H 82 " pdb=" CA GLU H 82 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 244 0.028 - 0.056: 160 0.056 - 0.084: 57 0.084 - 0.111: 25 0.111 - 0.139: 11 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO E 373 " pdb=" N PRO E 373 " pdb=" C PRO E 373 " pdb=" CB PRO E 373 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 494 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO L 60 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " -0.015 2.00e-02 2.50e+03 9.52e-03 2.27e+00 pdb=" CG TRP H 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS E 336 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO E 337 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " 0.019 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 234 2.74 - 3.28: 3348 3.28 - 3.82: 5244 3.82 - 4.36: 5995 4.36 - 4.90: 10460 Nonbonded interactions: 25281 Sorted by model distance: nonbonded pdb=" O ASN E 448 " pdb=" OG SER E 494 " model vdw 2.198 3.040 nonbonded pdb=" NZ LYS H 23 " pdb=" O THR H 76 " model vdw 2.242 3.120 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 115 " model vdw 2.263 3.040 nonbonded pdb=" O TYR H 108 " pdb=" OH TYR L 37 " model vdw 2.264 3.040 nonbonded pdb=" O ARG H 67 " pdb=" OG SER H 84 " model vdw 2.271 3.040 ... (remaining 25276 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: 0.030 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: 14.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.003 0.034 3392 Z= 0.193 Angle : 0.701 9.586 4614 Z= 0.378 Chirality : 0.044 0.139 497 Planarity : 0.005 0.039 601 Dihedral : 13.708 76.851 1202 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.35 (0.42), residues: 424 helix: -3.38 (0.98), residues: 18 sheet: 0.25 (0.50), residues: 131 loop : -1.37 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.001 0.000 HIS H 110 PHE 0.021 0.002 PHE E 497 TYR 0.018 0.001 TYR E 351 ARG 0.006 0.000 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.8997 (m-80) cc_final: 0.8779 (m-80) REVERT: E 467 ASP cc_start: 0.7961 (t70) cc_final: 0.7735 (t0) REVERT: H 29 PHE cc_start: 0.7613 (t80) cc_final: 0.7264 (t80) REVERT: H 67 ARG cc_start: 0.8905 (ptp-170) cc_final: 0.8544 (ttp-110) REVERT: L 39 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7662 (tp-100) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1825 time to fit residues: 21.2619 Evaluate side-chains 80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 50.0000 chunk 31 optimal weight: 0.0070 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 40.0000 chunk 32 optimal weight: 50.0000 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 30.0000 chunk 24 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 overall best weight: 3.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.127690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098145 restraints weight = 8956.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.101127 restraints weight = 5145.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102987 restraints weight = 3546.591| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3392 Z= 0.192 Angle : 0.699 10.162 4614 Z= 0.359 Chirality : 0.047 0.140 497 Planarity : 0.005 0.039 601 Dihedral : 5.443 19.414 471 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.95 % Allowed : 13.93 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.20 (0.42), residues: 424 helix: -3.51 (1.23), residues: 12 sheet: 0.24 (0.47), residues: 140 loop : -1.29 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 111 HIS 0.002 0.001 HIS H 110 PHE 0.023 0.002 PHE E 429 TYR 0.015 0.002 TYR E 449 ARG 0.007 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 346 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7629 (mtp85) REVERT: H 29 PHE cc_start: 0.7713 (t80) cc_final: 0.7267 (t80) REVERT: H 48 MET cc_start: 0.8304 (mmp) cc_final: 0.7683 (tpp) REVERT: H 67 ARG cc_start: 0.8812 (ptp-170) cc_final: 0.8587 (ttp-110) REVERT: L 39 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7710 (tp-100) outliers start: 7 outliers final: 4 residues processed: 84 average time/residue: 0.1750 time to fit residues: 17.3901 Evaluate side-chains 79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 40.0000 chunk 11 optimal weight: 40.0000 chunk 16 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 25 optimal weight: 40.0000 chunk 20 optimal weight: 30.0000 overall best weight: 22.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.118900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089682 restraints weight = 9156.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.092328 restraints weight = 5434.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.094046 restraints weight = 3856.138| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 3392 Z= 0.529 Angle : 0.861 11.256 4614 Z= 0.454 Chirality : 0.051 0.194 497 Planarity : 0.006 0.047 601 Dihedral : 6.472 19.980 471 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 2.79 % Allowed : 17.55 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.73 (0.40), residues: 424 helix: -3.56 (0.92), residues: 18 sheet: -0.09 (0.47), residues: 140 loop : -1.64 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.031 0.004 PHE E 338 TYR 0.015 0.002 TYR E 423 ARG 0.006 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: H 29 PHE cc_start: 0.8197 (t80) cc_final: 0.7711 (t80) REVERT: H 48 MET cc_start: 0.8266 (mmp) cc_final: 0.7920 (mmm) REVERT: H 67 ARG cc_start: 0.8898 (ptp-170) cc_final: 0.8668 (ttp-110) REVERT: L 46 LYS cc_start: 0.9592 (tppp) cc_final: 0.9356 (tppp) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.2314 time to fit residues: 21.6217 Evaluate side-chains 83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 108 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 chunk 39 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.126005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096338 restraints weight = 9380.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.099301 restraints weight = 5487.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.101174 restraints weight = 3834.157| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3392 Z= 0.225 Angle : 0.732 10.534 4614 Z= 0.375 Chirality : 0.047 0.150 497 Planarity : 0.005 0.045 601 Dihedral : 5.838 19.713 471 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.06 % Allowed : 20.06 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.60 (0.41), residues: 424 helix: -3.86 (0.76), residues: 24 sheet: 0.02 (0.47), residues: 140 loop : -1.45 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 111 HIS 0.006 0.001 HIS H 110 PHE 0.014 0.002 PHE E 338 TYR 0.016 0.002 TYR L 86 ARG 0.005 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7988 (t80) cc_final: 0.7402 (t80) REVERT: H 48 MET cc_start: 0.8278 (mmp) cc_final: 0.7690 (mmm) REVERT: H 67 ARG cc_start: 0.8827 (ptp-170) cc_final: 0.8598 (ttp-110) REVERT: L 36 TRP cc_start: 0.7918 (m100) cc_final: 0.7626 (m100) REVERT: L 39 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7620 (tp-100) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.1943 time to fit residues: 20.4684 Evaluate side-chains 87 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 40.0000 chunk 22 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 30 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 overall best weight: 6.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.4090 r_free = 0.4090 target = 0.130436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102184 restraints weight = 8884.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105060 restraints weight = 5212.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.106777 restraints weight = 3663.407| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3392 Z= 0.235 Angle : 0.731 10.905 4614 Z= 0.372 Chirality : 0.047 0.138 497 Planarity : 0.005 0.046 601 Dihedral : 5.752 19.551 471 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.90 % Allowed : 20.33 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.51 (0.41), residues: 424 helix: -3.36 (1.01), residues: 18 sheet: 0.02 (0.47), residues: 140 loop : -1.46 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 111 HIS 0.004 0.001 HIS H 110 PHE 0.012 0.002 PHE E 338 TYR 0.011 0.002 TYR L 86 ARG 0.005 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: E 474 GLN cc_start: 0.2929 (pp30) cc_final: 0.2522 (pp30) REVERT: H 29 PHE cc_start: 0.8052 (t80) cc_final: 0.7353 (t80) REVERT: H 48 MET cc_start: 0.8016 (mmp) cc_final: 0.7780 (mmm) REVERT: L 39 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7365 (tp-100) outliers start: 14 outliers final: 11 residues processed: 88 average time/residue: 0.1848 time to fit residues: 19.2065 Evaluate side-chains 91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 50.0000 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.4094 r_free = 0.4094 target = 0.130885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102574 restraints weight = 9124.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.105520 restraints weight = 5499.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107361 restraints weight = 3902.428| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3392 Z= 0.219 Angle : 0.715 11.318 4614 Z= 0.362 Chirality : 0.046 0.140 497 Planarity : 0.005 0.046 601 Dihedral : 5.657 20.588 471 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.90 % Allowed : 22.01 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.52 (0.41), residues: 424 helix: -3.53 (0.92), residues: 18 sheet: -0.03 (0.46), residues: 140 loop : -1.42 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 111 HIS 0.004 0.001 HIS H 110 PHE 0.017 0.002 PHE E 392 TYR 0.012 0.001 TYR E 351 ARG 0.005 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: H 29 PHE cc_start: 0.8016 (t80) cc_final: 0.7342 (t80) REVERT: H 48 MET cc_start: 0.7931 (mmp) cc_final: 0.7724 (mmm) REVERT: L 39 GLN cc_start: 0.7688 (tp-100) cc_final: 0.7332 (tp-100) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.1804 time to fit residues: 19.2954 Evaluate side-chains 91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 50.0000 chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.129830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101494 restraints weight = 9010.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.104398 restraints weight = 5310.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106232 restraints weight = 3748.913| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3392 Z= 0.250 Angle : 0.745 11.841 4614 Z= 0.376 Chirality : 0.047 0.153 497 Planarity : 0.005 0.046 601 Dihedral : 5.653 21.995 471 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.90 % Allowed : 23.12 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.60 (0.40), residues: 424 helix: -3.60 (0.86), residues: 18 sheet: -0.13 (0.46), residues: 139 loop : -1.45 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.015 0.002 PHE E 374 TYR 0.022 0.002 TYR E 351 ARG 0.006 0.001 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: H 29 PHE cc_start: 0.8065 (t80) cc_final: 0.7318 (t80) outliers start: 14 outliers final: 12 residues processed: 87 average time/residue: 0.1783 time to fit residues: 18.5202 Evaluate side-chains 91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 50.0000 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 35 optimal weight: 50.0000 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 36 optimal weight: 0.0970 chunk 14 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.4098 r_free = 0.4098 target = 0.131466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103513 restraints weight = 9244.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106581 restraints weight = 5383.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.108536 restraints weight = 3767.960| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3392 Z= 0.216 Angle : 0.737 10.610 4614 Z= 0.374 Chirality : 0.047 0.145 497 Planarity : 0.005 0.046 601 Dihedral : 5.579 22.255 471 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.18 % Allowed : 24.23 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.65 (0.40), residues: 424 helix: -3.54 (0.88), residues: 18 sheet: -0.19 (0.46), residues: 140 loop : -1.47 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.021 0.002 PHE E 497 TYR 0.019 0.002 TYR E 351 ARG 0.007 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7935 (t80) cc_final: 0.7189 (t80) REVERT: H 38 ARG cc_start: 0.8663 (ptt90) cc_final: 0.8305 (ptt90) outliers start: 15 outliers final: 14 residues processed: 90 average time/residue: 0.1807 time to fit residues: 19.3292 Evaluate side-chains 94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 50.0000 chunk 28 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.4090 r_free = 0.4090 target = 0.130562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.101771 restraints weight = 9036.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104847 restraints weight = 5180.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106829 restraints weight = 3618.840| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3392 Z= 0.239 Angle : 0.747 8.383 4614 Z= 0.381 Chirality : 0.047 0.148 497 Planarity : 0.005 0.046 601 Dihedral : 5.586 22.387 471 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.90 % Allowed : 24.79 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.74 (0.40), residues: 424 helix: -3.65 (0.87), residues: 18 sheet: -0.32 (0.46), residues: 140 loop : -1.49 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.020 0.002 PHE E 429 TYR 0.022 0.002 TYR E 351 ARG 0.007 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7968 (t80) cc_final: 0.7163 (t80) outliers start: 14 outliers final: 14 residues processed: 87 average time/residue: 0.2010 time to fit residues: 20.9683 Evaluate side-chains 94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 0.0670 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 40 optimal weight: 8.9990 chunk 14 optimal weight: 40.0000 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.132411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104497 restraints weight = 9109.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107655 restraints weight = 5223.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.109604 restraints weight = 3622.427| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3392 Z= 0.196 Angle : 0.728 7.156 4614 Z= 0.371 Chirality : 0.047 0.141 497 Planarity : 0.005 0.046 601 Dihedral : 5.422 22.439 471 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.34 % Allowed : 26.46 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.49 (0.41), residues: 424 helix: -3.91 (0.63), residues: 25 sheet: -0.22 (0.46), residues: 141 loop : -1.13 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 111 HIS 0.004 0.001 HIS H 110 PHE 0.021 0.002 PHE E 374 TYR 0.023 0.002 TYR E 351 ARG 0.011 0.001 ARG H 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 90 average time/residue: 0.1825 time to fit residues: 19.4382 Evaluate side-chains 94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 50.0000 chunk 34 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 19 optimal weight: 0.1980 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 40.0000 chunk 38 optimal weight: 50.0000 chunk 37 optimal weight: 9.9990 chunk 14 optimal weight: 50.0000 overall best weight: 6.6388 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.131241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.103160 restraints weight = 9384.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.106313 restraints weight = 5447.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.108275 restraints weight = 3809.412| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3392 Z= 0.243 Angle : 0.750 7.740 4614 Z= 0.385 Chirality : 0.047 0.150 497 Planarity : 0.005 0.046 601 Dihedral : 5.586 21.806 471 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.62 % Allowed : 26.46 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.51 (0.42), residues: 424 helix: -3.65 (0.85), residues: 18 sheet: -0.21 (0.47), residues: 139 loop : -1.29 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 111 HIS 0.004 0.001 HIS H 110 PHE 0.024 0.003 PHE H 29 TYR 0.022 0.002 TYR E 351 ARG 0.006 0.001 ARG L 17 =============================================================================== Job complete usr+sys time: 1343.21 seconds wall clock time: 24 minutes 28.68 seconds (1468.68 seconds total)