Starting phenix.real_space_refine (version: dev) on Mon Apr 4 11:36:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/04_2022/7k45_22660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/04_2022/7k45_22660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/04_2022/7k45_22660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/04_2022/7k45_22660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/04_2022/7k45_22660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k45_22660/04_2022/7k45_22660.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 3038 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 849 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "L" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 730 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 96, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1431 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.37, per 1000 atoms: 0.78 Number of scatterers: 3038 At special positions: 0 Unit cell: (70.35, 55.65, 100.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 533 8.00 N 529 7.00 C 1960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.10 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 494.7 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 10 sheets defined 15.3% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.745A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.815A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.227A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.295A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.052A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.738A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 126 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 933 1.33 - 1.47: 940 1.47 - 1.60: 1225 1.60 - 1.73: 2 1.73 - 1.86: 18 Bond restraints: 3118 Sorted by residual: bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.611 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.10e-02 8.26e+03 1.59e+01 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.435 1.474 -0.039 1.10e-02 8.26e+03 1.27e+01 bond pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.00e-02 1.00e+04 1.01e+01 bond pdb=" NE1 TRP H 50 " pdb=" CE2 TRP H 50 " ideal model delta sigma weight residual 1.370 1.337 0.033 1.10e-02 8.26e+03 8.78e+00 ... (remaining 3113 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.20: 78 105.20 - 112.42: 1419 112.42 - 119.64: 1023 119.64 - 126.87: 1718 126.87 - 134.09: 29 Bond angle restraints: 4267 Sorted by residual: angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.03 128.19 -8.16 9.90e-01 1.02e+00 6.79e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 120.21 126.95 -6.74 9.60e-01 1.09e+00 4.93e+01 angle pdb=" C SER B 383 " pdb=" N PRO B 384 " pdb=" CA PRO B 384 " ideal model delta sigma weight residual 119.56 126.42 -6.86 1.02e+00 9.61e-01 4.53e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.56 126.33 -6.77 1.02e+00 9.61e-01 4.41e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.87 126.70 -6.83 1.04e+00 9.25e-01 4.31e+01 ... (remaining 4262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 1722 16.65 - 33.30: 55 33.30 - 49.94: 10 49.94 - 66.59: 4 66.59 - 83.24: 1 Dihedral angle restraints: 1792 sinusoidal: 588 harmonic: 1204 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 121.87 -28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 66.25 26.75 1 1.00e+01 1.00e-02 1.03e+01 dihedral pdb=" C TYR L 92 " pdb=" N TYR L 92 " pdb=" CA TYR L 92 " pdb=" CB TYR L 92 " ideal model delta harmonic sigma weight residual -122.60 -115.16 -7.44 0 2.50e+00 1.60e-01 8.85e+00 ... (remaining 1789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 307 0.068 - 0.136: 127 0.136 - 0.204: 30 0.204 - 0.272: 2 0.272 - 0.340: 4 Chirality restraints: 470 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.64e+01 chirality pdb=" C2 NAG A 2 " pdb=" C1 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" N2 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.83 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C2 NAG A 1 " pdb=" C1 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" N2 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 467 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.030 2.00e-02 2.50e+03 1.51e-02 4.56e+00 pdb=" CG TYR L 92 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 50 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.49e+00 pdb=" CG TRP H 50 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP H 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 50 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP H 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 50 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 50 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 50 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 50 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.023 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP H 47 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.017 2.00e-02 2.50e+03 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 1766 3.03 - 3.50: 2712 3.50 - 3.97: 4880 3.97 - 4.43: 5575 4.43 - 4.90: 9162 Nonbonded interactions: 24095 Sorted by model distance: nonbonded pdb=" N LYS B 462 " pdb=" O LYS B 462 " model vdw 2.568 2.496 nonbonded pdb=" N GLU L 80 " pdb=" O GLU L 80 " model vdw 2.592 2.496 nonbonded pdb=" CB GLN H 6 " pdb=" OE1 GLN H 6 " model vdw 2.598 2.752 nonbonded pdb=" N GLY B 502 " pdb=" O GLY B 502 " model vdw 2.601 2.496 nonbonded pdb=" N SER B 373 " pdb=" N PHE B 374 " model vdw 2.605 2.560 ... (remaining 24090 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 1960 2.51 5 N 529 2.21 5 O 533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.710 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: 25.580 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.060 Process input model: 16.070 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.014 0.092 3118 Z= 0.956 Angle : 1.411 8.157 4267 Z= 0.973 Chirality : 0.078 0.340 470 Planarity : 0.006 0.039 560 Dihedral : 9.473 83.236 1007 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.41), residues: 411 helix: -4.00 (0.49), residues: 33 sheet: 1.14 (0.43), residues: 150 loop : 1.17 (0.40), residues: 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.425 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2044 time to fit residues: 19.7879 Evaluate side-chains 43 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 23 optimal weight: 0.0770 chunk 37 optimal weight: 0.0980 overall best weight: 0.1338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 3118 Z= 0.254 Angle : 0.665 6.588 4267 Z= 0.362 Chirality : 0.047 0.141 470 Planarity : 0.005 0.057 560 Dihedral : 4.961 22.059 472 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.41), residues: 411 helix: -3.71 (0.64), residues: 27 sheet: 0.74 (0.41), residues: 150 loop : 0.88 (0.40), residues: 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.1699 time to fit residues: 12.6128 Evaluate side-chains 50 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.360 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0320 time to fit residues: 0.8042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.101 3118 Z= 0.531 Angle : 0.777 7.768 4267 Z= 0.432 Chirality : 0.050 0.152 470 Planarity : 0.006 0.066 560 Dihedral : 5.304 19.711 472 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.40), residues: 411 helix: -3.32 (0.99), residues: 20 sheet: 0.27 (0.40), residues: 152 loop : 0.36 (0.38), residues: 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.375 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.1791 time to fit residues: 11.2210 Evaluate side-chains 41 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0428 time to fit residues: 0.6501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 3118 Z= 0.295 Angle : 0.700 11.537 4267 Z= 0.390 Chirality : 0.048 0.181 470 Planarity : 0.006 0.052 560 Dihedral : 4.965 22.557 472 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.41), residues: 411 helix: -2.99 (1.01), residues: 21 sheet: 0.16 (0.40), residues: 152 loop : 0.49 (0.40), residues: 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.354 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.2137 time to fit residues: 12.9730 Evaluate side-chains 47 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0396 time to fit residues: 0.7187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.0050 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.0040 chunk 7 optimal weight: 0.7980 overall best weight: 0.2524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 3118 Z= 0.254 Angle : 0.700 14.120 4267 Z= 0.388 Chirality : 0.047 0.175 470 Planarity : 0.005 0.055 560 Dihedral : 4.668 20.266 472 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.41), residues: 411 helix: -2.80 (1.04), residues: 21 sheet: 0.26 (0.41), residues: 148 loop : 0.44 (0.41), residues: 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.358 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 0.1910 time to fit residues: 11.3947 Evaluate side-chains 44 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0346 time to fit residues: 0.5490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 32 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 13 optimal weight: 0.0870 chunk 20 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 overall best weight: 0.1314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.123 3118 Z= 0.228 Angle : 0.704 15.882 4267 Z= 0.400 Chirality : 0.046 0.176 470 Planarity : 0.005 0.064 560 Dihedral : 4.338 16.353 472 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.42), residues: 411 helix: -2.53 (1.05), residues: 21 sheet: 0.18 (0.41), residues: 152 loop : 0.49 (0.42), residues: 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.367 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 0.2127 time to fit residues: 11.8171 Evaluate side-chains 44 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0393 time to fit residues: 0.5347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.221 3118 Z= 0.350 Angle : 0.789 20.548 4267 Z= 0.465 Chirality : 0.047 0.248 470 Planarity : 0.005 0.063 560 Dihedral : 4.365 16.993 472 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.42), residues: 411 helix: -2.56 (1.04), residues: 21 sheet: 0.16 (0.41), residues: 151 loop : 0.41 (0.42), residues: 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.357 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.2112 time to fit residues: 11.1906 Evaluate side-chains 44 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0306 time to fit residues: 0.6468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 3118 Z= 0.261 Angle : 0.686 14.408 4267 Z= 0.387 Chirality : 0.046 0.179 470 Planarity : 0.005 0.084 560 Dihedral : 4.432 17.266 472 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.42), residues: 411 helix: -2.61 (1.03), residues: 21 sheet: 0.08 (0.42), residues: 145 loop : 0.40 (0.42), residues: 245 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.361 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 0.2169 time to fit residues: 12.1835 Evaluate side-chains 42 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0342 time to fit residues: 0.5270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.0370 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 0.0870 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 0.773 3118 Z= 1.266 Angle : 1.302 53.796 4267 Z= 0.751 Chirality : 0.059 0.819 470 Planarity : 0.004 0.036 560 Dihedral : 4.283 16.750 472 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.42), residues: 411 helix: -2.64 (1.01), residues: 21 sheet: 0.12 (0.41), residues: 146 loop : 0.39 (0.43), residues: 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.361 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.2155 time to fit residues: 11.1599 Evaluate side-chains 42 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0311 time to fit residues: 0.5272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 0.904 3118 Z= 1.456 Angle : 1.492 77.302 4267 Z= 0.784 Chirality : 0.058 0.764 470 Planarity : 0.005 0.061 560 Dihedral : 4.546 18.115 472 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.42), residues: 411 helix: -3.07 (1.04), residues: 14 sheet: 0.11 (0.42), residues: 150 loop : 0.28 (0.42), residues: 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.359 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.2142 time to fit residues: 10.9316 Evaluate side-chains 40 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 23 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 15 optimal weight: 0.0980 chunk 40 optimal weight: 0.0050 overall best weight: 0.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.101085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091758 restraints weight = 7211.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.094145 restraints weight = 4195.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095766 restraints weight = 2769.954| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 0.905 3118 Z= 1.440 Angle : 1.406 71.211 4267 Z= 0.753 Chirality : 0.058 0.796 470 Planarity : 0.008 0.141 560 Dihedral : 4.210 15.872 472 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.43), residues: 411 helix: -2.65 (1.01), residues: 21 sheet: 0.21 (0.43), residues: 146 loop : 0.33 (0.42), residues: 244 =============================================================================== Job complete usr+sys time: 1451.19 seconds wall clock time: 26 minutes 40.51 seconds (1600.51 seconds total)