Starting phenix.real_space_refine on Sat Apr 26 23:20:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i52_4410/04_2025/6i52_4410.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i52_4410/04_2025/6i52_4410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6i52_4410/04_2025/6i52_4410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i52_4410/04_2025/6i52_4410.map" model { file = "/net/cci-nas-00/data/ceres_data/6i52_4410/04_2025/6i52_4410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i52_4410/04_2025/6i52_4410.cif" } resolution = 4.7 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= 0.002 sd= 0.012 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 P 20 5.49 5 S 16 5.16 5 C 2377 2.51 5 N 635 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3856 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 966 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1041 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1449 Classifications: {'peptide': 178} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 171} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 400 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 3.41, per 1000 atoms: 0.88 Number of scatterers: 3856 At special positions: 0 Unit cell: (82.68, 65.72, 107.06, 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) S 16 16.00 P 20 15.00 O 808 8.00 N 635 7.00 C 2377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 503.4 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: 828 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 22.9% alpha, 24.1% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 3.969A pdb=" N ILE A 13 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 14 " --> pdb=" O THR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.682A pdb=" N LYS A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.704A pdb=" N LEU B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.590A pdb=" N GLN C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 450 through 455' Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.646A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 557 Processing helix chain 'C' and resid 561 through 571 Processing helix chain 'C' and resid 604 through 617 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 6.827A pdb=" N ARG A 78 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 89 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.877A pdb=" N ILE A 37 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.712A pdb=" N SER B 61 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.131A pdb=" N GLY B 73 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 134 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 468 through 476 removed outlier: 4.815A pdb=" N ILE C 473 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE C 526 " --> pdb=" O ILE C 473 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N GLN C 531 " --> pdb=" O ILE C 592 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N TYR C 594 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP C 533 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL C 596 " --> pdb=" O TRP C 533 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR C 535 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASN C 598 " --> pdb=" O THR C 535 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 591 " --> pdb=" O ASP C 584 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 584 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 580 " --> pdb=" O THR C 595 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG C 578 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 599 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP C 576 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 482 through 484 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 497 108 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 1.30 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: 1129 1.34 - 1.45: 627 1.45 - 1.57: 2136 1.57 - 1.69: 39 1.69 - 1.81: 23 Bond restraints: 3954 Sorted by residual: bond pdb=" C THR B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.49e+00 bond pdb=" C ALA C 482 " pdb=" N TYR C 483 " ideal model delta sigma weight residual 1.331 1.356 -0.025 2.07e-02 2.33e+03 1.40e+00 bond pdb=" C3' DT D 11 " pdb=" O3' DT D 11 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" N ARG C 460 " pdb=" CA ARG C 460 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.90e-02 2.77e+03 1.04e+00 bond pdb=" N ALA B 177 " pdb=" CA ALA B 177 " ideal model delta sigma weight residual 1.468 1.457 0.012 1.24e-02 6.50e+03 8.68e-01 ... (remaining 3949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5238 1.39 - 2.78: 159 2.78 - 4.17: 24 4.17 - 5.56: 6 5.56 - 6.95: 2 Bond angle restraints: 5429 Sorted by residual: angle pdb=" C GLY C 459 " pdb=" N ARG C 460 " pdb=" CA ARG C 460 " ideal model delta sigma weight residual 121.70 128.65 -6.95 1.80e+00 3.09e-01 1.49e+01 angle pdb=" C GLU C 462 " pdb=" N LYS C 463 " pdb=" CA LYS C 463 " ideal model delta sigma weight residual 123.05 117.73 5.32 1.40e+00 5.10e-01 1.45e+01 angle pdb=" C PHE C 466 " pdb=" N PHE C 467 " pdb=" CA PHE C 467 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.55e+00 angle pdb=" C ILE B 85 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " ideal model delta sigma weight residual 122.67 118.18 4.49 1.73e+00 3.34e-01 6.74e+00 angle pdb=" C ASP C 465 " pdb=" N PHE C 466 " pdb=" CA PHE C 466 " ideal model delta sigma weight residual 121.54 126.29 -4.75 1.91e+00 2.74e-01 6.18e+00 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.30: 2228 29.30 - 58.61: 90 58.61 - 87.91: 15 87.91 - 117.21: 2 117.21 - 146.51: 3 Dihedral angle restraints: 2338 sinusoidal: 1070 harmonic: 1268 Sorted by residual: dihedral pdb=" CA GLU C 462 " pdb=" C GLU C 462 " pdb=" N LYS C 463 " pdb=" CA LYS C 463 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PHE C 466 " pdb=" C PHE C 466 " pdb=" N PHE C 467 " pdb=" CA PHE C 467 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DT D 11 " pdb=" C3' DT D 11 " pdb=" O3' DT D 11 " pdb=" P DT D 12 " ideal model delta sinusoidal sigma weight residual 220.00 73.49 146.51 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 2335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 396 0.027 - 0.054: 137 0.054 - 0.081: 40 0.081 - 0.109: 31 0.109 - 0.136: 14 Chirality restraints: 618 Sorted by residual: chirality pdb=" CA THR B 79 " pdb=" N THR B 79 " pdb=" C THR B 79 " pdb=" CB THR B 79 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE A 24 " pdb=" N ILE A 24 " pdb=" C ILE A 24 " pdb=" CB ILE A 24 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 615 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 79 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C THR B 79 " 0.043 2.00e-02 2.50e+03 pdb=" O THR B 79 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP B 80 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 30 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 31 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 118 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 119 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.019 5.00e-02 4.00e+02 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1101 2.82 - 3.34: 3351 3.34 - 3.86: 6120 3.86 - 4.38: 6724 4.38 - 4.90: 11453 Nonbonded interactions: 28749 Sorted by model distance: nonbonded pdb=" OD2 ASP A 9 " pdb=" OG1 THR A 11 " model vdw 2.303 3.040 nonbonded pdb=" ND1 HIS B 68 " pdb=" O GLY B 138 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP C 500 " pdb=" N GLY C 501 " model vdw 2.330 3.120 nonbonded pdb=" OG SER C 474 " pdb=" O SER C 524 " model vdw 2.339 3.040 nonbonded pdb=" O VAL B 163 " pdb=" ND1 HIS B 166 " model vdw 2.361 3.120 ... (remaining 28744 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: 0.200 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.040 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: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5551 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 : 0.002 0.050 3954 Z= 0.120 Angle : 0.571 6.949 5429 Z= 0.339 Chirality : 0.039 0.136 618 Planarity : 0.004 0.047 639 Dihedral : 16.564 146.514 1510 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.94 % Allowed : 11.56 % Favored : 87.50 % Rotamer: Outliers : 5.70 % Allowed : 9.84 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -4.07 (0.31), residues: 424 helix: -3.47 (0.33), residues: 95 sheet: -1.85 (0.49), residues: 77 loop : -2.75 (0.30), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 533 HIS 0.002 0.000 HIS B 166 PHE 0.016 0.001 PHE C 467 TYR 0.010 0.001 TYR B 151 ARG 0.001 0.000 ARG C 591 Details of bonding type rmsd hydrogen bonds : bond 0.15029 ( 108) hydrogen bonds : angle 12.38356 ( 294) covalent geometry : bond 0.00244 ( 3954) covalent geometry : angle 0.57147 ( 5429) *********************** 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 134 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.6038 (OUTLIER) cc_final: 0.5038 (mp10) REVERT: A 53 MET cc_start: 0.6572 (mtm) cc_final: 0.6343 (mpp) REVERT: A 75 PHE cc_start: 0.7684 (t80) cc_final: 0.7453 (t80) REVERT: B 160 PHE cc_start: 0.6461 (p90) cc_final: 0.6220 (p90) REVERT: B 167 HIS cc_start: 0.8149 (m-70) cc_final: 0.7539 (t-170) REVERT: C 478 VAL cc_start: 0.4301 (OUTLIER) cc_final: 0.3902 (t) REVERT: C 479 ASP cc_start: 0.8308 (m-30) cc_final: 0.7717 (p0) REVERT: C 531 GLN cc_start: 0.7691 (pt0) cc_final: 0.7128 (tm-30) outliers start: 22 outliers final: 6 residues processed: 129 average time/residue: 0.1803 time to fit residues: 27.8243 Evaluate side-chains 54 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 80 ASN C 516 ASN C 531 GLN C 561 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.099767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.078391 restraints weight = 29033.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.079594 restraints weight = 24952.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.080361 restraints weight = 22185.255| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3954 Z= 0.199 Angle : 0.766 8.570 5429 Z= 0.418 Chirality : 0.047 0.189 618 Planarity : 0.006 0.049 639 Dihedral : 19.520 146.829 657 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.08 % Favored : 92.22 % Rotamer: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -3.13 (0.33), residues: 424 helix: -1.31 (0.47), residues: 90 sheet: -1.16 (0.53), residues: 81 loop : -2.83 (0.30), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 101 HIS 0.005 0.002 HIS B 167 PHE 0.020 0.003 PHE A 75 TYR 0.016 0.002 TYR B 151 ARG 0.007 0.001 ARG C 593 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 108) hydrogen bonds : angle 8.21176 ( 294) covalent geometry : bond 0.00400 ( 3954) covalent geometry : angle 0.76640 ( 5429) *********************** 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 66 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: B 128 PHE cc_start: 0.6898 (m-10) cc_final: 0.6625 (m-80) REVERT: B 135 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8544 (mmtt) REVERT: B 154 ILE cc_start: 0.6824 (pt) cc_final: 0.6437 (pt) REVERT: B 160 PHE cc_start: 0.6886 (p90) cc_final: 0.6665 (p90) REVERT: B 167 HIS cc_start: 0.8366 (m-70) cc_final: 0.8163 (m-70) REVERT: C 536 LEU cc_start: 0.9192 (mp) cc_final: 0.8854 (mp) REVERT: C 584 ASP cc_start: 0.8721 (m-30) cc_final: 0.8252 (p0) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.1688 time to fit residues: 13.7760 Evaluate side-chains 41 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 0.0170 chunk 3 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 overall best weight: 0.8424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.100651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.082678 restraints weight = 36373.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.083306 restraints weight = 33964.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.083771 restraints weight = 32159.796| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3954 Z= 0.135 Angle : 0.653 7.231 5429 Z= 0.354 Chirality : 0.044 0.195 618 Planarity : 0.005 0.051 639 Dihedral : 19.557 147.488 657 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.55 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.34), residues: 424 helix: -0.77 (0.48), residues: 91 sheet: -0.78 (0.56), residues: 79 loop : -2.69 (0.31), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 517 HIS 0.004 0.001 HIS B 67 PHE 0.010 0.002 PHE B 71 TYR 0.018 0.002 TYR B 151 ARG 0.005 0.001 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 108) hydrogen bonds : angle 7.41146 ( 294) covalent geometry : bond 0.00291 ( 3954) covalent geometry : angle 0.65267 ( 5429) *********************** 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 67 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.5823 (mpp) cc_final: 0.5409 (mmt) REVERT: B 128 PHE cc_start: 0.7269 (m-10) cc_final: 0.7048 (m-80) REVERT: B 135 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8459 (pptt) REVERT: B 137 PHE cc_start: 0.8556 (m-80) cc_final: 0.8090 (m-80) REVERT: B 154 ILE cc_start: 0.6767 (pt) cc_final: 0.6431 (pt) REVERT: B 160 PHE cc_start: 0.6956 (p90) cc_final: 0.6514 (p90) REVERT: C 523 ILE cc_start: 0.9639 (pt) cc_final: 0.9294 (pt) REVERT: C 572 MET cc_start: 0.7539 (ptt) cc_final: 0.7337 (ppp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1440 time to fit residues: 12.2666 Evaluate side-chains 42 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 37 ASN B 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.098578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.080611 restraints weight = 38072.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.081270 restraints weight = 35344.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.081778 restraints weight = 33160.172| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3954 Z= 0.156 Angle : 0.679 6.751 5429 Z= 0.368 Chirality : 0.044 0.191 618 Planarity : 0.005 0.051 639 Dihedral : 19.685 146.567 657 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.73 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.36), residues: 424 helix: -0.45 (0.50), residues: 88 sheet: -0.80 (0.58), residues: 82 loop : -2.42 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 533 HIS 0.007 0.002 HIS B 167 PHE 0.012 0.002 PHE A 75 TYR 0.017 0.002 TYR C 610 ARG 0.006 0.001 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 108) hydrogen bonds : angle 7.34633 ( 294) covalent geometry : bond 0.00336 ( 3954) covalent geometry : angle 0.67878 ( 5429) *********************** 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 61 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.5832 (mpp) cc_final: 0.5557 (mmt) REVERT: A 75 PHE cc_start: 0.7770 (t80) cc_final: 0.7478 (t80) REVERT: B 160 PHE cc_start: 0.6974 (p90) cc_final: 0.6692 (p90) REVERT: C 536 LEU cc_start: 0.9250 (mp) cc_final: 0.9041 (mp) REVERT: C 584 ASP cc_start: 0.8448 (m-30) cc_final: 0.7975 (p0) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1393 time to fit residues: 11.0016 Evaluate side-chains 38 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 0 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.093790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.074594 restraints weight = 39094.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.075492 restraints weight = 35122.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.076229 restraints weight = 32288.960| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3954 Z= 0.161 Angle : 0.701 7.082 5429 Z= 0.378 Chirality : 0.045 0.197 618 Planarity : 0.005 0.052 639 Dihedral : 19.555 147.020 657 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.14 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.36), residues: 424 helix: -0.39 (0.51), residues: 90 sheet: -0.81 (0.59), residues: 82 loop : -2.57 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 72 HIS 0.004 0.002 HIS B 167 PHE 0.013 0.002 PHE B 71 TYR 0.017 0.002 TYR B 151 ARG 0.005 0.001 ARG C 578 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 108) hydrogen bonds : angle 6.98065 ( 294) covalent geometry : bond 0.00354 ( 3954) covalent geometry : angle 0.70135 ( 5429) *********************** 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 53 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5994 (mpp) cc_final: 0.5746 (mmt) REVERT: B 160 PHE cc_start: 0.7096 (p90) cc_final: 0.6867 (p90) REVERT: C 532 LEU cc_start: 0.6745 (tp) cc_final: 0.6203 (mm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1520 time to fit residues: 10.3460 Evaluate side-chains 36 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.090477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.072122 restraints weight = 39374.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.072922 restraints weight = 35665.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.073518 restraints weight = 32939.476| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5517 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3954 Z= 0.182 Angle : 0.736 6.945 5429 Z= 0.399 Chirality : 0.045 0.197 618 Planarity : 0.005 0.051 639 Dihedral : 19.885 146.682 657 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.61 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.36), residues: 424 helix: -0.44 (0.50), residues: 88 sheet: -1.04 (0.56), residues: 82 loop : -2.53 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 72 HIS 0.004 0.002 HIS B 62 PHE 0.018 0.002 PHE B 71 TYR 0.018 0.002 TYR B 151 ARG 0.013 0.001 ARG C 578 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 108) hydrogen bonds : angle 7.23847 ( 294) covalent geometry : bond 0.00399 ( 3954) covalent geometry : angle 0.73564 ( 5429) *********************** 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 52 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: B 160 PHE cc_start: 0.7188 (p90) cc_final: 0.6710 (p90) REVERT: C 536 LEU cc_start: 0.8979 (mp) cc_final: 0.8705 (mp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1677 time to fit residues: 11.0782 Evaluate side-chains 38 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 40.0000 chunk 28 optimal weight: 30.0000 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 20 optimal weight: 40.0000 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 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 = 0.4035 r_free = 0.4035 target = 0.089227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.071988 restraints weight = 39186.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.072578 restraints weight = 36470.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.073024 restraints weight = 34352.019| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.7657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3954 Z= 0.168 Angle : 0.725 7.091 5429 Z= 0.389 Chirality : 0.046 0.196 618 Planarity : 0.005 0.050 639 Dihedral : 19.951 148.174 657 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.61 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.36), residues: 424 helix: -0.58 (0.48), residues: 92 sheet: -0.94 (0.57), residues: 82 loop : -2.64 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 72 HIS 0.003 0.001 HIS B 62 PHE 0.013 0.002 PHE B 71 TYR 0.019 0.002 TYR C 610 ARG 0.004 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 108) hydrogen bonds : angle 6.81165 ( 294) covalent geometry : bond 0.00368 ( 3954) covalent geometry : angle 0.72475 ( 5429) *********************** 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 49 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 59 ILE cc_start: 0.7598 (mp) cc_final: 0.7391 (mp) REVERT: A 63 MET cc_start: 0.5901 (mmp) cc_final: 0.5219 (mmt) REVERT: B 160 PHE cc_start: 0.7069 (p90) cc_final: 0.6469 (p90) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1527 time to fit residues: 9.5844 Evaluate side-chains 33 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 43 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 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 = 0.3913 r_free = 0.3913 target = 0.083434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.067813 restraints weight = 41861.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.068222 restraints weight = 39535.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.068565 restraints weight = 37702.253| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.9019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3954 Z= 0.247 Angle : 0.908 8.404 5429 Z= 0.491 Chirality : 0.052 0.335 618 Planarity : 0.006 0.041 639 Dihedral : 20.253 146.844 657 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 28.75 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.79 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -3.50 (0.34), residues: 424 helix: -1.68 (0.42), residues: 89 sheet: -1.39 (0.52), residues: 91 loop : -3.09 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 72 HIS 0.011 0.003 HIS B 166 PHE 0.018 0.003 PHE A 87 TYR 0.024 0.003 TYR C 610 ARG 0.004 0.001 ARG C 591 Details of bonding type rmsd hydrogen bonds : bond 0.04989 ( 108) hydrogen bonds : angle 7.63492 ( 294) covalent geometry : bond 0.00536 ( 3954) covalent geometry : angle 0.90834 ( 5429) *********************** 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 44 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.415 Fit side-chains REVERT: C 586 TYR cc_start: 0.8152 (t80) cc_final: 0.7906 (t80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1613 time to fit residues: 9.0823 Evaluate side-chains 33 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 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 = 0.3961 r_free = 0.3961 target = 0.086103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.070384 restraints weight = 41476.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.070946 restraints weight = 38429.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.071421 restraints weight = 35950.465| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.9074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3954 Z= 0.182 Angle : 0.797 8.478 5429 Z= 0.427 Chirality : 0.049 0.214 618 Planarity : 0.005 0.045 639 Dihedral : 20.334 149.508 657 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.08 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -3.39 (0.34), residues: 424 helix: -1.07 (0.49), residues: 85 sheet: -1.87 (0.50), residues: 85 loop : -2.96 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 72 HIS 0.008 0.002 HIS B 166 PHE 0.020 0.002 PHE A 75 TYR 0.019 0.002 TYR B 151 ARG 0.003 0.001 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 108) hydrogen bonds : angle 7.01391 ( 294) covalent geometry : bond 0.00399 ( 3954) covalent geometry : angle 0.79713 ( 5429) *********************** 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 47 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.470 Fit side-chains REVERT: A 59 ILE cc_start: 0.7448 (mp) cc_final: 0.7208 (mp) REVERT: A 63 MET cc_start: 0.5702 (mmp) cc_final: 0.5034 (mmt) REVERT: B 160 PHE cc_start: 0.7070 (p90) cc_final: 0.6658 (p90) REVERT: C 586 TYR cc_start: 0.8143 (t80) cc_final: 0.7936 (t80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1629 time to fit residues: 9.8761 Evaluate side-chains 39 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.0070 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 overall best weight: 3.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 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 = 0.3988 r_free = 0.3988 target = 0.088214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.071597 restraints weight = 39734.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.072132 restraints weight = 36860.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.072504 restraints weight = 34823.339| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.9166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3954 Z= 0.154 Angle : 0.724 7.586 5429 Z= 0.392 Chirality : 0.047 0.217 618 Planarity : 0.005 0.042 639 Dihedral : 20.221 150.346 657 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.61 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -3.01 (0.37), residues: 424 helix: -0.70 (0.49), residues: 91 sheet: -1.81 (0.47), residues: 101 loop : -2.71 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 533 HIS 0.006 0.001 HIS B 166 PHE 0.019 0.002 PHE A 75 TYR 0.018 0.002 TYR B 151 ARG 0.003 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 108) hydrogen bonds : angle 6.73578 ( 294) covalent geometry : bond 0.00339 ( 3954) covalent geometry : angle 0.72371 ( 5429) ********************** 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 51 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.432 Fit side-chains REVERT: A 59 ILE cc_start: 0.7421 (mp) cc_final: 0.7208 (mp) REVERT: A 63 MET cc_start: 0.6048 (mmp) cc_final: 0.5601 (mmt) REVERT: B 160 PHE cc_start: 0.7059 (p90) cc_final: 0.6713 (p90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1603 time to fit residues: 10.6051 Evaluate side-chains 36 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 0.0970 chunk 8 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.090965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.074072 restraints weight = 38467.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.074601 restraints weight = 35538.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.075126 restraints weight = 33427.099| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.9349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3954 Z= 0.155 Angle : 0.740 9.195 5429 Z= 0.402 Chirality : 0.047 0.201 618 Planarity : 0.005 0.043 639 Dihedral : 20.215 150.484 657 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.38 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.37), residues: 424 helix: -0.88 (0.48), residues: 91 sheet: -1.68 (0.48), residues: 101 loop : -2.57 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 533 HIS 0.005 0.001 HIS B 166 PHE 0.017 0.002 PHE A 75 TYR 0.019 0.002 TYR B 151 ARG 0.003 0.001 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 108) hydrogen bonds : angle 6.93988 ( 294) covalent geometry : bond 0.00339 ( 3954) covalent geometry : angle 0.73976 ( 5429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.03 seconds wall clock time: 28 minutes 22.84 seconds (1702.84 seconds total)