Starting phenix.real_space_refine on Thu Dec 7 19:15:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/12_2023/6i52_4410.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/12_2023/6i52_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/12_2023/6i52_4410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/12_2023/6i52_4410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/12_2023/6i52_4410.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i52_4410/12_2023/6i52_4410.pdb" } 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 Residue "A ASP 91": "OD1" <-> "OD2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C ASP 465": "OD1" <-> "OD2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "C ARG 582": "NH1" <-> "NH2" Residue "C ARG 605": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.76, per 1000 atoms: 0.72 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 - 3.50 Amino acid : False - 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: 1.41 Conformation dependent library (CDL) restraints added in 770.0 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: 1.17 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: 1.01 Time building geometry restraints manager: 1.53 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: 100.90 - 107.53: 206 107.53 - 114.15: 2239 114.15 - 120.78: 1583 120.78 - 127.41: 1373 127.41 - 134.03: 28 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 2.440 nonbonded pdb=" ND1 HIS B 68 " pdb=" O GLY B 138 " model vdw 2.326 2.520 nonbonded pdb=" OD1 ASP C 500 " pdb=" N GLY C 501 " model vdw 2.330 2.520 nonbonded pdb=" OG SER C 474 " pdb=" O SER C 524 " model vdw 2.339 2.440 nonbonded pdb=" O VAL B 163 " pdb=" ND1 HIS B 166 " model vdw 2.361 2.520 ... (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 ========== 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: 0.060 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: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.560 Find NCS groups from input model: 0.110 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 6 residues processed: 129 average time/residue: 0.1819 time to fit residues: 28.0354 Evaluate side-chains 51 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0400 time to fit residues: 0.9821 ------------------------------------------------------------------------------- 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: 6.9990 chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 0.0070 overall best weight: 4.0204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN C 454 GLN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3954 Z= 0.234 Angle : 0.735 8.335 5429 Z= 0.398 Chirality : 0.045 0.185 618 Planarity : 0.005 0.051 639 Dihedral : 19.475 146.669 657 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.31 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % 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: -3.08 (0.33), residues: 424 helix: -1.31 (0.48), residues: 90 sheet: -1.18 (0.52), residues: 77 loop : -2.73 (0.30), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 101 HIS 0.004 0.001 HIS B 166 PHE 0.011 0.002 PHE A 75 TYR 0.014 0.002 TYR B 151 ARG 0.004 0.001 ARG C 578 *********************** 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 68 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1749 time to fit residues: 14.7040 Evaluate side-chains 38 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 0.0670 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN C 516 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 0.4764 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= 0.185 Angle : 0.646 6.914 5429 Z= 0.351 Chirality : 0.043 0.188 618 Planarity : 0.005 0.058 639 Dihedral : 19.584 147.319 657 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.02 % Favored : 91.27 % Rotamer: Outliers : 0.26 % Allowed : 3.37 % 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: -2.60 (0.36), residues: 424 helix: -0.64 (0.51), residues: 89 sheet: -0.76 (0.57), residues: 78 loop : -2.58 (0.33), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 517 HIS 0.009 0.002 HIS B 167 PHE 0.018 0.002 PHE A 75 TYR 0.015 0.002 TYR B 151 ARG 0.003 0.000 ARG A 22 *********************** 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 69 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.1726 time to fit residues: 15.0330 Evaluate side-chains 43 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 0.0980 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3954 Z= 0.178 Angle : 0.647 7.229 5429 Z= 0.349 Chirality : 0.043 0.208 618 Planarity : 0.004 0.048 639 Dihedral : 19.573 147.074 657 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.25 % Favored : 91.04 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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 (0.35), residues: 424 helix: -0.75 (0.50), residues: 92 sheet: -0.98 (0.57), residues: 80 loop : -2.57 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 517 HIS 0.004 0.001 HIS B 67 PHE 0.010 0.001 PHE B 71 TYR 0.022 0.002 TYR B 151 ARG 0.003 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 fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1536 time to fit residues: 11.5555 Evaluate side-chains 41 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.0170 chunk 8 optimal weight: 0.0870 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3954 Z= 0.192 Angle : 0.651 7.327 5429 Z= 0.352 Chirality : 0.043 0.213 618 Planarity : 0.004 0.052 639 Dihedral : 19.625 146.718 657 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.78 % Favored : 91.51 % 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: -2.52 (0.35), residues: 424 helix: -0.47 (0.49), residues: 92 sheet: -0.96 (0.56), residues: 80 loop : -2.51 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 72 HIS 0.003 0.001 HIS B 67 PHE 0.014 0.002 PHE B 137 TYR 0.021 0.002 TYR B 151 ARG 0.005 0.001 ARG C 593 *********************** 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 62 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.430 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1510 time to fit residues: 11.9298 Evaluate side-chains 38 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 40.0000 chunk 42 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.6741 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= 0.242 Angle : 0.727 7.316 5429 Z= 0.393 Chirality : 0.045 0.219 618 Planarity : 0.005 0.053 639 Dihedral : 19.972 146.106 657 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.43 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: -2.52 (0.36), residues: 424 helix: -0.21 (0.50), residues: 90 sheet: -1.12 (0.55), residues: 80 loop : -2.54 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 533 HIS 0.007 0.002 HIS B 68 PHE 0.014 0.002 PHE B 71 TYR 0.019 0.002 TYR B 151 ARG 0.006 0.001 ARG A 7 *********************** 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 54 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1828 time to fit residues: 12.7140 Evaluate side-chains 37 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 28 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.6850 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= 0.203 Angle : 0.687 7.332 5429 Z= 0.374 Chirality : 0.044 0.209 618 Planarity : 0.004 0.045 639 Dihedral : 19.992 147.334 657 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.20 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -0.19 (0.50), residues: 92 sheet: -1.15 (0.55), residues: 82 loop : -2.54 (0.33), 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 166 PHE 0.013 0.002 PHE B 71 TYR 0.020 0.002 TYR B 151 ARG 0.006 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 57 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1614 time to fit residues: 11.8610 Evaluate side-chains 38 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 0.3980 chunk 33 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 ASN C 531 GLN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.7675 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= 0.248 Angle : 0.751 7.258 5429 Z= 0.407 Chirality : 0.045 0.209 618 Planarity : 0.005 0.043 639 Dihedral : 20.224 146.921 657 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.61 % Favored : 88.68 % 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: -2.68 (0.36), residues: 424 helix: -0.45 (0.49), residues: 91 sheet: -0.76 (0.58), residues: 75 loop : -2.76 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 72 HIS 0.005 0.002 HIS B 166 PHE 0.020 0.002 PHE A 75 TYR 0.020 0.003 TYR B 151 ARG 0.007 0.001 ARG A 60 *********************** 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 54 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1575 time to fit residues: 10.9530 Evaluate side-chains 37 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.7907 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= 0.211 Angle : 0.717 7.828 5429 Z= 0.387 Chirality : 0.045 0.200 618 Planarity : 0.004 0.042 639 Dihedral : 20.250 148.362 657 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.61 % Favored : 88.68 % 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: -2.59 (0.37), residues: 424 helix: -0.35 (0.49), residues: 93 sheet: -1.15 (0.55), residues: 84 loop : -2.61 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 533 HIS 0.004 0.001 HIS B 67 PHE 0.015 0.002 PHE A 75 TYR 0.021 0.002 TYR B 151 ARG 0.003 0.001 ARG A 7 *********************** 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 54 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1526 time to fit residues: 10.5777 Evaluate side-chains 34 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.8033 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= 0.212 Angle : 0.715 7.080 5429 Z= 0.385 Chirality : 0.045 0.216 618 Planarity : 0.004 0.039 639 Dihedral : 20.238 148.937 657 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.85 % Favored : 88.44 % 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: -2.55 (0.37), residues: 424 helix: -0.40 (0.51), residues: 93 sheet: -1.11 (0.55), residues: 84 loop : -2.54 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 533 HIS 0.003 0.001 HIS B 67 PHE 0.014 0.002 PHE B 71 TYR 0.018 0.002 TYR B 151 ARG 0.003 0.000 ARG A 7 ********************** 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 49 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.448 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1633 time to fit residues: 10.3260 Evaluate side-chains 33 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.0000 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 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 = 0.4070 r_free = 0.4070 target = 0.093620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.075095 restraints weight = 36032.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.075526 restraints weight = 33493.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.076026 restraints weight = 31819.999| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.8211 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= 0.200 Angle : 0.704 7.320 5429 Z= 0.378 Chirality : 0.045 0.190 618 Planarity : 0.004 0.037 639 Dihedral : 20.203 149.429 657 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 19.96 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: -2.46 (0.38), residues: 424 helix: -0.29 (0.52), residues: 93 sheet: -1.13 (0.58), residues: 80 loop : -2.45 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 533 HIS 0.003 0.001 HIS B 166 PHE 0.014 0.002 PHE B 71 TYR 0.019 0.002 TYR B 151 ARG 0.003 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1067.43 seconds wall clock time: 20 minutes 17.31 seconds (1217.31 seconds total)