Starting phenix.real_space_refine on Tue Feb 11 02:42:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i52_4410/02_2025/6i52_4410.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i52_4410/02_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_4410/02_2025/6i52_4410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i52_4410/02_2025/6i52_4410.map" model { file = "/net/cci-nas-00/data/ceres_data/6i52_4410/02_2025/6i52_4410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i52_4410/02_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-5592/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: 2.90, per 1000 atoms: 0.75 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: 0.90 Conformation dependent library (CDL) restraints added in 431.6 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: 1.30 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: 1.04 Time building geometry restraints manager: 1.08 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: 0.130 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: 0.030 Process input model: 14.770 Find NCS groups from input model: 0.050 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- 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= 0.163 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 *********************** 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 : 0.431 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: 0.1864 time to fit residues: 28.6878 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 : 0.440 ------------------------------------------------------------------------------- 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: 6.9990 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 = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.078391 restraints weight = 29033.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.079589 restraints weight = 24935.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.080555 restraints weight = 22174.233| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 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= 0.257 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 *********************** 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 : 0.440 Fit side-chains revert: symmetry clash REVERT: B 128 PHE cc_start: 0.7025 (m-10) cc_final: 0.6798 (m-80) REVERT: B 135 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8589 (mmtt) REVERT: B 154 ILE cc_start: 0.6903 (pt) cc_final: 0.6540 (pt) REVERT: B 160 PHE cc_start: 0.6925 (p90) cc_final: 0.6710 (p90) REVERT: C 536 LEU cc_start: 0.9176 (mp) cc_final: 0.8847 (mp) REVERT: C 584 ASP cc_start: 0.8714 (m-30) cc_final: 0.8219 (p0) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.1759 time to fit residues: 14.2711 Evaluate side-chains 40 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 0.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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** B 167 HIS C 492 ASN C 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.099111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.079666 restraints weight = 36805.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.080468 restraints weight = 33814.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.081112 restraints weight = 31480.766| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.4946 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= 0.195 Angle : 0.653 6.905 5429 Z= 0.356 Chirality : 0.044 0.185 618 Planarity : 0.005 0.052 639 Dihedral : 19.592 147.541 657 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.31 % Favored : 91.98 % 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: -2.66 (0.35), residues: 424 helix: -0.67 (0.49), residues: 89 sheet: -0.91 (0.55), residues: 81 loop : -2.60 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 517 HIS 0.010 0.002 HIS B 167 PHE 0.010 0.002 PHE C 577 TYR 0.016 0.002 TYR B 151 ARG 0.004 0.001 ARG A 7 *********************** 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 : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.5842 (mpp) cc_final: 0.5433 (mmt) REVERT: B 128 PHE cc_start: 0.7349 (m-10) cc_final: 0.7109 (m-80) REVERT: B 160 PHE cc_start: 0.7051 (p90) cc_final: 0.6494 (p90) REVERT: C 523 ILE cc_start: 0.9673 (pt) cc_final: 0.9346 (pt) REVERT: C 584 ASP cc_start: 0.8987 (m-30) cc_final: 0.8427 (p0) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1498 time to fit residues: 12.7366 Evaluate side-chains 43 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.098586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.080584 restraints weight = 37459.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.081256 restraints weight = 34603.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.081802 restraints weight = 32479.546| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3954 Z= 0.192 Angle : 0.666 7.060 5429 Z= 0.360 Chirality : 0.043 0.203 618 Planarity : 0.005 0.063 639 Dihedral : 19.687 146.719 657 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.02 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -2.53 (0.36), residues: 424 helix: -0.66 (0.49), residues: 90 sheet: -0.81 (0.58), residues: 82 loop : -2.49 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 533 HIS 0.004 0.001 HIS B 67 PHE 0.011 0.002 PHE A 75 TYR 0.016 0.002 TYR B 151 ARG 0.004 0.000 ARG A 22 *********************** 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 59 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5870 (mpp) cc_final: 0.5560 (mmt) REVERT: A 75 PHE cc_start: 0.7603 (t80) cc_final: 0.7316 (t80) REVERT: B 160 PHE cc_start: 0.6997 (p90) cc_final: 0.6793 (p90) REVERT: C 536 LEU cc_start: 0.9298 (mp) cc_final: 0.9093 (mp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1508 time to fit residues: 11.5252 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 : 0.408 ------------------------------------------------------------------------------- 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: 0.7980 chunk 5 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.098457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.081220 restraints weight = 39263.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.081891 restraints weight = 36189.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.082436 restraints weight = 33820.620| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3954 Z= 0.214 Angle : 0.680 7.545 5429 Z= 0.369 Chirality : 0.043 0.182 618 Planarity : 0.005 0.052 639 Dihedral : 19.794 147.096 657 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.14 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: -2.47 (0.36), residues: 424 helix: -0.37 (0.51), residues: 92 sheet: -0.73 (0.60), residues: 82 loop : -2.59 (0.32), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 533 HIS 0.005 0.001 HIS B 167 PHE 0.020 0.002 PHE B 71 TYR 0.018 0.002 TYR B 151 ARG 0.005 0.000 ARG C 578 *********************** 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 57 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 135 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8560 (mmmt) REVERT: B 160 PHE cc_start: 0.7038 (p90) cc_final: 0.6789 (p90) REVERT: C 536 LEU cc_start: 0.9171 (mp) cc_final: 0.8936 (mp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1451 time to fit residues: 10.5755 Evaluate side-chains 35 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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: 9.9990 chunk 39 optimal weight: 0.0570 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.7704 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.092257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.075084 restraints weight = 37214.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.075886 restraints weight = 33433.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.076509 restraints weight = 30641.528| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.6795 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= 0.217 Angle : 0.692 7.320 5429 Z= 0.375 Chirality : 0.044 0.215 618 Planarity : 0.005 0.063 639 Dihedral : 19.971 147.170 657 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.49 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -2.51 (0.37), residues: 424 helix: -0.37 (0.51), residues: 92 sheet: -0.97 (0.58), residues: 82 loop : -2.55 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 72 HIS 0.005 0.002 HIS B 167 PHE 0.014 0.002 PHE B 71 TYR 0.021 0.002 TYR B 151 ARG 0.006 0.001 ARG C 578 *********************** 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 55 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.478 Fit side-chains REVERT: B 160 PHE cc_start: 0.7007 (p90) cc_final: 0.6712 (p90) REVERT: C 536 LEU cc_start: 0.9323 (mp) cc_final: 0.9060 (mp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1605 time to fit residues: 11.1910 Evaluate side-chains 34 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 0.0980 chunk 42 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 6.0188 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.088178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.070977 restraints weight = 39382.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.071574 restraints weight = 36441.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.072046 restraints weight = 34243.761| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.7633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3954 Z= 0.281 Angle : 0.776 8.188 5429 Z= 0.417 Chirality : 0.047 0.219 618 Planarity : 0.006 0.059 639 Dihedral : 20.168 146.833 657 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.56 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -2.67 (0.37), residues: 424 helix: -0.57 (0.50), residues: 90 sheet: -1.11 (0.57), residues: 82 loop : -2.59 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 72 HIS 0.012 0.002 HIS B 166 PHE 0.017 0.002 PHE B 71 TYR 0.022 0.003 TYR B 151 ARG 0.004 0.001 ARG A 7 *********************** 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 46 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 118 TYR cc_start: 0.8870 (m-80) cc_final: 0.8380 (p90) REVERT: C 536 LEU cc_start: 0.9319 (mp) cc_final: 0.9041 (mp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1665 time to fit residues: 9.7354 Evaluate side-chains 32 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 20.0000 chunk 25 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 7.7590 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.083918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.068371 restraints weight = 41656.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.068848 restraints weight = 38920.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.069153 restraints weight = 36850.766| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.9062 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= 0.342 Angle : 0.913 13.876 5429 Z= 0.490 Chirality : 0.052 0.246 618 Planarity : 0.006 0.043 639 Dihedral : 20.762 146.541 657 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 27.28 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.79 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: -3.35 (0.34), residues: 424 helix: -1.15 (0.49), residues: 85 sheet: -1.64 (0.53), residues: 76 loop : -2.95 (0.32), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 72 HIS 0.006 0.002 HIS C 600 PHE 0.021 0.003 PHE B 86 TYR 0.025 0.003 TYR C 610 ARG 0.007 0.001 ARG B 99 *********************** 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 45 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: B 160 PHE cc_start: 0.6764 (p90) cc_final: 0.6497 (p90) REVERT: C 586 TYR cc_start: 0.8149 (t80) cc_final: 0.7892 (t80) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1666 time to fit residues: 9.5121 Evaluate side-chains 34 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 0.0470 chunk 33 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 overall best weight: 2.9882 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.088144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.070745 restraints weight = 38951.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.071352 restraints weight = 35909.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.071872 restraints weight = 33595.448| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.8885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3954 Z= 0.232 Angle : 0.766 11.552 5429 Z= 0.407 Chirality : 0.047 0.197 618 Planarity : 0.005 0.046 639 Dihedral : 20.709 149.659 657 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.14 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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 (0.35), residues: 424 helix: -0.83 (0.50), residues: 87 sheet: -1.28 (0.56), residues: 78 loop : -2.96 (0.32), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 533 HIS 0.005 0.002 HIS B 62 PHE 0.017 0.002 PHE A 75 TYR 0.022 0.002 TYR B 151 ARG 0.004 0.001 ARG A 60 *********************** 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 : 0.452 Fit side-chains revert: symmetry clash REVERT: A 59 ILE cc_start: 0.7370 (mp) cc_final: 0.7046 (mp) REVERT: A 63 MET cc_start: 0.4790 (mmp) cc_final: 0.3822 (mmt) REVERT: B 160 PHE cc_start: 0.6623 (p90) cc_final: 0.6363 (p90) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1649 time to fit residues: 9.9160 Evaluate side-chains 35 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 6.9990 chunk 12 optimal weight: 0.0020 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.086301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.069551 restraints weight = 39982.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.070096 restraints weight = 37024.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.070504 restraints weight = 34912.646| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.9210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3954 Z= 0.253 Angle : 0.787 11.224 5429 Z= 0.418 Chirality : 0.047 0.215 618 Planarity : 0.005 0.045 639 Dihedral : 20.813 149.173 657 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 20.36 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: -3.14 (0.35), residues: 424 helix: -0.85 (0.46), residues: 93 sheet: -1.31 (0.56), residues: 78 loop : -2.99 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 533 HIS 0.003 0.001 HIS C 600 PHE 0.014 0.002 PHE A 75 TYR 0.021 0.003 TYR B 151 ARG 0.003 0.001 ARG C 591 ********************** 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 48 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.394 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1651 time to fit residues: 10.1917 Evaluate side-chains 34 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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: 6.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.087901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.071109 restraints weight = 38799.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.071638 restraints weight = 36294.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.072037 restraints weight = 34334.002| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.9353 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= 0.231 Angle : 0.773 10.497 5429 Z= 0.415 Chirality : 0.047 0.214 618 Planarity : 0.005 0.045 639 Dihedral : 20.861 150.301 657 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.38 % Favored : 88.92 % 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: -3.02 (0.37), residues: 424 helix: -0.93 (0.48), residues: 91 sheet: -1.52 (0.54), residues: 87 loop : -2.72 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 533 HIS 0.004 0.001 HIS C 600 PHE 0.016 0.002 PHE A 75 TYR 0.021 0.002 TYR B 151 ARG 0.004 0.001 ARG C 578 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1502.81 seconds wall clock time: 27 minutes 59.24 seconds (1679.24 seconds total)