Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:36:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/11_2022/7t01_25574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/11_2022/7t01_25574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/11_2022/7t01_25574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/11_2022/7t01_25574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/11_2022/7t01_25574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/11_2022/7t01_25574.pdb" } resolution = 2.69 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 "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3343 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Time building chain proxies: 2.37, per 1000 atoms: 0.71 Number of scatterers: 3343 At special positions: 0 Unit cell: (68.85, 62.37, 101.25, 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 636 8.00 N 555 7.00 C 2136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 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: 1.30 Conformation dependent library (CDL) restraints added in 508.9 milliseconds 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 13.1% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.007A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.380A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.572A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.297A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.732A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.596A pdb=" N GLN H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR H 70 " --> pdb=" O THR H 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.602A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR H 54 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL H 34 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL H 112 " --> pdb=" O HIS H 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.602A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR H 54 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL H 34 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.714A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.722A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA L 50 " --> pdb=" O ARG L 53 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 255 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: 0.85 Time building geometry restraints manager: 1.45 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: 1049 1.34 - 1.46: 894 1.46 - 1.59: 1469 1.59 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 3432 Sorted by residual: bond pdb=" C THR L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.75e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.75e+00 bond pdb=" C LYS H 13 " pdb=" N PRO H 14 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.07e+00 bond pdb=" CB ILE L 48 " pdb=" CG2 ILE L 48 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 1.00e+00 ... (remaining 3427 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.85: 120 106.85 - 113.65: 1789 113.65 - 120.45: 1284 120.45 - 127.25: 1439 127.25 - 134.05: 41 Bond angle restraints: 4673 Sorted by residual: angle pdb=" CA LEU H 29 " pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 116.30 129.39 -13.09 3.50e+00 8.16e-02 1.40e+01 angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 120.52 -6.62 1.80e+00 3.09e-01 1.35e+01 angle pdb=" CA VAL L 29 " pdb=" CB VAL L 29 " pdb=" CG1 VAL L 29 " ideal model delta sigma weight residual 110.40 116.34 -5.94 1.70e+00 3.46e-01 1.22e+01 angle pdb=" N VAL L 29 " pdb=" CA VAL L 29 " pdb=" CB VAL L 29 " ideal model delta sigma weight residual 112.08 107.07 5.01 1.68e+00 3.54e-01 8.90e+00 angle pdb=" C TYR L 49 " pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " ideal model delta sigma weight residual 110.90 106.38 4.52 1.58e+00 4.01e-01 8.19e+00 ... (remaining 4668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 1810 14.74 - 29.48: 171 29.48 - 44.22: 29 44.22 - 58.96: 5 58.96 - 73.70: 4 Dihedral angle restraints: 2019 sinusoidal: 781 harmonic: 1238 Sorted by residual: dihedral pdb=" CA TYR H 54 " pdb=" C TYR H 54 " pdb=" N TRP H 55 " pdb=" CA TRP H 55 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA SER L 9 " pdb=" C SER L 9 " pdb=" N SER L 10 " pdb=" CA SER L 10 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LEU L 78 " pdb=" C LEU L 78 " pdb=" N GLN L 79 " pdb=" CA GLN L 79 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 311 0.043 - 0.085: 143 0.085 - 0.128: 51 0.128 - 0.171: 8 0.171 - 0.214: 2 Chirality restraints: 515 Sorted by residual: chirality pdb=" CA THR L 94 " pdb=" N THR L 94 " pdb=" C THR L 94 " pdb=" CB THR L 94 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASER L 7 " pdb=" N SER L 7 " pdb=" C SER L 7 " pdb=" CB ASER L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" C PRO H 14 " pdb=" CB PRO H 14 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 512 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " -0.025 2.00e-02 2.50e+03 2.08e-02 8.61e+00 pdb=" CG TYR L 49 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 29 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C VAL L 29 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL L 29 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE L 30 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 60 " -0.167 9.50e-02 1.11e+02 7.55e-02 4.40e+00 pdb=" NE ARG H 60 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 60 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG H 60 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG H 60 " -0.000 2.00e-02 2.50e+03 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 1135 2.85 - 3.36: 3020 3.36 - 3.87: 5498 3.87 - 4.39: 6364 4.39 - 4.90: 10848 Nonbonded interactions: 26865 Sorted by model distance: nonbonded pdb=" OD2 ASP H 74 " pdb=" OG SER H 76 " model vdw 2.335 2.440 nonbonded pdb=" O ALA L 25 " pdb=" OG1 THR L 69 " model vdw 2.379 2.440 nonbonded pdb=" ND2 ASN A 394 " pdb=" OE2 GLU A 516 " model vdw 2.419 2.520 nonbonded pdb=" OG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 2.485 2.440 nonbonded pdb=" NH1 ARG H 60 " pdb=" OG1 THR L 94 " model vdw 2.508 2.520 ... (remaining 26860 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 2136 2.51 5 N 555 2.21 5 O 636 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.140 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: 25.910 Check model and map are aligned: 0.060 Convert atoms to be neutral: 1.330 Process input model: 19.700 Find NCS groups from input model: 0.110 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:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.004 0.039 3432 Z= 0.241 Angle : 0.870 13.094 4673 Z= 0.469 Chirality : 0.054 0.214 515 Planarity : 0.008 0.075 598 Dihedral : 12.300 73.703 1220 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.38), residues: 422 helix: -3.82 (0.72), residues: 19 sheet: -0.35 (0.44), residues: 125 loop : -0.63 (0.35), residues: 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.7492 time to fit residues: 131.6656 Evaluate side-chains 145 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 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 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3432 Z= 0.267 Angle : 0.763 9.812 4673 Z= 0.376 Chirality : 0.049 0.183 515 Planarity : 0.005 0.032 598 Dihedral : 6.601 23.775 465 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 5.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.38), residues: 422 helix: -1.58 (1.41), residues: 18 sheet: -0.03 (0.45), residues: 125 loop : -0.66 (0.33), residues: 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 153 average time/residue: 0.7535 time to fit residues: 120.1335 Evaluate side-chains 149 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 2 residues processed: 7 average time/residue: 0.0617 time to fit residues: 1.1480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 3432 Z= 0.371 Angle : 0.772 10.665 4673 Z= 0.384 Chirality : 0.050 0.191 515 Planarity : 0.005 0.040 598 Dihedral : 6.314 23.769 465 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 5.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.38), residues: 422 helix: -1.70 (1.34), residues: 18 sheet: -0.09 (0.45), residues: 131 loop : -0.78 (0.34), residues: 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 150 average time/residue: 0.8084 time to fit residues: 125.8953 Evaluate side-chains 154 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.0473 time to fit residues: 0.8260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 3432 Z= 0.417 Angle : 0.798 11.140 4673 Z= 0.397 Chirality : 0.051 0.203 515 Planarity : 0.005 0.047 598 Dihedral : 6.299 25.943 465 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 5.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.39), residues: 422 helix: -1.89 (1.31), residues: 18 sheet: -0.28 (0.48), residues: 117 loop : -0.95 (0.35), residues: 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 158 average time/residue: 0.7382 time to fit residues: 121.2716 Evaluate side-chains 152 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 5 average time/residue: 0.3286 time to fit residues: 2.3225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 3432 Z= 0.319 Angle : 0.780 11.665 4673 Z= 0.381 Chirality : 0.050 0.189 515 Planarity : 0.005 0.044 598 Dihedral : 6.022 26.003 465 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 5.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.39), residues: 422 helix: -2.05 (1.30), residues: 19 sheet: -0.56 (0.46), residues: 123 loop : -0.87 (0.36), residues: 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 162 average time/residue: 0.7435 time to fit residues: 125.3793 Evaluate side-chains 164 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.3122 time to fit residues: 2.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.0770 chunk 40 optimal weight: 0.3980 chunk 33 optimal weight: 0.0670 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.0170 chunk 13 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.1914 ------------------------------------------------------------------------------- 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: 0.8375 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3432 Z= 0.230 Angle : 0.796 12.366 4673 Z= 0.382 Chirality : 0.051 0.331 515 Planarity : 0.005 0.045 598 Dihedral : 5.773 25.412 465 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 6.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.40), residues: 422 helix: -2.41 (1.23), residues: 19 sheet: -0.76 (0.48), residues: 122 loop : -0.74 (0.36), residues: 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 163 average time/residue: 0.7659 time to fit residues: 129.9510 Evaluate side-chains 157 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 10 average time/residue: 0.0376 time to fit residues: 1.1152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.0670 chunk 16 optimal weight: 0.0050 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3432 Z= 0.291 Angle : 0.812 12.258 4673 Z= 0.393 Chirality : 0.050 0.181 515 Planarity : 0.006 0.048 598 Dihedral : 5.835 28.042 465 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 6.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.40), residues: 422 helix: -2.44 (1.26), residues: 19 sheet: -0.99 (0.47), residues: 124 loop : -0.73 (0.37), residues: 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 160 average time/residue: 0.7345 time to fit residues: 122.3536 Evaluate side-chains 163 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 10 average time/residue: 0.0692 time to fit residues: 1.5583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.8396 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 3432 Z= 0.315 Angle : 0.834 13.051 4673 Z= 0.405 Chirality : 0.051 0.247 515 Planarity : 0.006 0.060 598 Dihedral : 5.872 28.244 465 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 4.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.41), residues: 422 helix: -2.49 (1.27), residues: 19 sheet: -0.95 (0.48), residues: 124 loop : -0.78 (0.38), residues: 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 0.403 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 158 average time/residue: 0.7674 time to fit residues: 126.0388 Evaluate side-chains 155 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 7 average time/residue: 0.0460 time to fit residues: 1.0114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.0000 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 overall best weight: 0.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 3432 Z= 0.228 Angle : 0.850 13.045 4673 Z= 0.411 Chirality : 0.050 0.250 515 Planarity : 0.005 0.051 598 Dihedral : 5.526 23.554 465 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.41), residues: 422 helix: -2.72 (1.16), residues: 19 sheet: -1.02 (0.47), residues: 124 loop : -0.87 (0.38), residues: 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 154 average time/residue: 0.7661 time to fit residues: 122.6062 Evaluate side-chains 147 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 5 average time/residue: 0.0764 time to fit residues: 0.9861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 3432 Z= 0.339 Angle : 0.895 12.609 4673 Z= 0.434 Chirality : 0.051 0.268 515 Planarity : 0.006 0.070 598 Dihedral : 5.730 24.226 465 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.62 (0.41), residues: 422 helix: -2.43 (1.28), residues: 19 sheet: -1.08 (0.47), residues: 126 loop : -0.95 (0.38), residues: 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.406 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 150 average time/residue: 0.7735 time to fit residues: 120.5119 Evaluate side-chains 149 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 3 average time/residue: 0.0992 time to fit residues: 0.9430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 28 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.077706 restraints weight = 7431.820| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.88 r_work: 0.3335 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work: 0.3315 rms_B_bonded: 2.65 restraints_weight: 0.1250 r_work: 0.3305 rms_B_bonded: 2.70 restraints_weight: 0.0625 r_work: 0.3294 rms_B_bonded: 2.78 restraints_weight: 0.0312 r_work: 0.3282 rms_B_bonded: 2.89 restraints_weight: 0.0156 r_work: 0.3270 rms_B_bonded: 3.02 restraints_weight: 0.0078 r_work: 0.3258 rms_B_bonded: 3.17 restraints_weight: 0.0039 r_work: 0.3244 rms_B_bonded: 3.34 restraints_weight: 0.0020 r_work: 0.3230 rms_B_bonded: 3.54 restraints_weight: 0.0010 r_work: 0.3216 rms_B_bonded: 3.76 restraints_weight: 0.0005 r_work: 0.3200 rms_B_bonded: 4.00 restraints_weight: 0.0002 r_work: 0.3184 rms_B_bonded: 4.28 restraints_weight: 0.0001 r_work: 0.3167 rms_B_bonded: 4.58 restraints_weight: 0.0001 r_work: 0.3148 rms_B_bonded: 4.92 restraints_weight: 0.0000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 3432 Z= 0.311 Angle : 0.918 13.527 4673 Z= 0.437 Chirality : 0.050 0.231 515 Planarity : 0.006 0.062 598 Dihedral : 5.640 24.269 465 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.41), residues: 422 helix: -3.20 (0.94), residues: 25 sheet: -1.14 (0.46), residues: 126 loop : -1.02 (0.39), residues: 271 =============================================================================== Job complete usr+sys time: 2691.33 seconds wall clock time: 48 minutes 14.47 seconds (2894.47 seconds total)