Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 20:56:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/10_2023/7t01_25574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/10_2023/7t01_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_25574/10_2023/7t01_25574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/10_2023/7t01_25574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/10_2023/7t01_25574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/10_2023/7t01_25574.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-1.21rc1-5097/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: 2.40, per 1000 atoms: 0.72 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: 1.21 Conformation dependent library (CDL) restraints added in 422.5 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: 0.40 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: 0.92 Time building geometry restraints manager: 1.34 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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 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: 25.990 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.160 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.7926 time to fit residues: 139.0790 Evaluate side-chains 145 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5176 ------------------------------------------------------------------------------- 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: 0.4980 chunk 17 optimal weight: 0.0470 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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: 0.8176 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3432 Z= 0.268 Angle : 0.756 9.572 4673 Z= 0.372 Chirality : 0.048 0.179 515 Planarity : 0.005 0.031 598 Dihedral : 6.432 23.412 465 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.36 % Allowed : 18.77 % Favored : 75.87 % 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: -0.79 (0.38), residues: 422 helix: -1.47 (1.43), residues: 18 sheet: -0.04 (0.45), residues: 125 loop : -0.68 (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 166 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 150 average time/residue: 0.7541 time to fit residues: 117.7994 Evaluate side-chains 147 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.0633 time to fit residues: 1.0103 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 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 3 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8202 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3432 Z= 0.297 Angle : 0.759 11.273 4673 Z= 0.375 Chirality : 0.049 0.184 515 Planarity : 0.005 0.040 598 Dihedral : 6.099 23.390 465 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.09 % Allowed : 25.20 % Favored : 69.71 % 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: -1.02 (0.39), residues: 422 helix: -1.79 (1.94), residues: 12 sheet: -0.40 (0.47), residues: 123 loop : -0.75 (0.34), residues: 287 *********************** 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 166 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 153 average time/residue: 0.8898 time to fit residues: 140.9691 Evaluate side-chains 153 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 6 average time/residue: 0.0485 time to fit residues: 0.9618 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 78 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8253 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3432 Z= 0.435 Angle : 0.809 11.162 4673 Z= 0.399 Chirality : 0.052 0.217 515 Planarity : 0.005 0.046 598 Dihedral : 6.240 25.291 465 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 6.43 % Allowed : 28.15 % Favored : 65.42 % 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: -1.91 (1.86), residues: 12 sheet: -0.38 (0.48), residues: 115 loop : -0.93 (0.35), residues: 295 *********************** 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 164 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 146 average time/residue: 0.8928 time to fit residues: 135.0191 Evaluate side-chains 149 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.3354 time to fit residues: 2.3243 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 13 optimal weight: 0.0020 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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: 0.8220 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3432 Z= 0.301 Angle : 0.787 11.556 4673 Z= 0.380 Chirality : 0.049 0.188 515 Planarity : 0.005 0.047 598 Dihedral : 5.943 25.381 465 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 6.97 % Allowed : 28.95 % Favored : 64.08 % 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: -1.28 (0.40), residues: 422 helix: -2.09 (1.29), residues: 19 sheet: -0.84 (0.46), residues: 125 loop : -0.73 (0.37), residues: 278 *********************** 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 182 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 162 average time/residue: 0.8286 time to fit residues: 139.3645 Evaluate side-chains 160 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 8 average time/residue: 0.2182 time to fit residues: 2.4914 ------------------------------------------------------------------------------- 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: 0.4980 chunk 40 optimal weight: 0.2980 chunk 33 optimal weight: 0.0020 chunk 18 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.1988 ------------------------------------------------------------------------------- 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: 0.8178 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3432 Z= 0.223 Angle : 0.799 12.635 4673 Z= 0.376 Chirality : 0.048 0.173 515 Planarity : 0.005 0.049 598 Dihedral : 5.633 24.075 465 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.63 % Allowed : 35.66 % Favored : 58.71 % 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: -1.22 (0.40), residues: 422 helix: -1.96 (1.87), residues: 12 sheet: -0.76 (0.47), residues: 122 loop : -0.76 (0.36), residues: 288 *********************** 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 177 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 162 average time/residue: 0.8195 time to fit residues: 137.8362 Evaluate side-chains 163 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 6 residues processed: 10 average time/residue: 0.0425 time to fit residues: 1.2067 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 3432 Z= 0.434 Angle : 0.855 12.234 4673 Z= 0.418 Chirality : 0.051 0.194 515 Planarity : 0.006 0.050 598 Dihedral : 6.096 26.448 465 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 5.90 % Allowed : 35.12 % Favored : 58.98 % 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: -1.44 (0.40), residues: 422 helix: -2.40 (1.30), residues: 19 sheet: -0.86 (0.47), residues: 118 loop : -0.88 (0.37), residues: 285 *********************** 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 172 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 159 average time/residue: 0.7743 time to fit residues: 128.1655 Evaluate side-chains 158 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.0417 time to fit residues: 0.9078 ------------------------------------------------------------------------------- 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: 0.5980 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.0270 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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: 0.8221 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3432 Z= 0.325 Angle : 0.855 12.595 4673 Z= 0.410 Chirality : 0.051 0.279 515 Planarity : 0.006 0.051 598 Dihedral : 5.887 25.916 465 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.83 % Allowed : 37.80 % Favored : 57.37 % 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: -1.42 (0.41), residues: 422 helix: -2.47 (1.29), residues: 19 sheet: -0.92 (0.47), residues: 122 loop : -0.82 (0.37), residues: 281 *********************** 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 166 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 155 average time/residue: 0.8804 time to fit residues: 141.5823 Evaluate side-chains 156 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 5 average time/residue: 0.0756 time to fit residues: 0.9647 ------------------------------------------------------------------------------- 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: 0.1980 chunk 37 optimal weight: 0.0370 chunk 24 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 overall best weight: 0.1436 ------------------------------------------------------------------------------- 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: 0.8165 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3432 Z= 0.226 Angle : 0.848 13.133 4673 Z= 0.404 Chirality : 0.050 0.240 515 Planarity : 0.006 0.058 598 Dihedral : 5.545 24.183 465 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.95 % Allowed : 40.75 % Favored : 56.30 % 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: -1.51 (0.41), residues: 422 helix: -3.03 (1.15), residues: 19 sheet: -1.03 (0.46), residues: 124 loop : -0.81 (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 161 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 157 average time/residue: 0.7421 time to fit residues: 121.3958 Evaluate side-chains 152 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 0.0693 time to fit residues: 0.8098 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 overall best weight: 0.2580 ------------------------------------------------------------------------------- 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: 0.8167 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3432 Z= 0.262 Angle : 0.880 12.799 4673 Z= 0.417 Chirality : 0.049 0.262 515 Planarity : 0.006 0.053 598 Dihedral : 5.550 23.865 465 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.68 % Allowed : 40.75 % Favored : 56.57 % 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: -1.52 (0.42), residues: 422 helix: -3.47 (0.89), residues: 25 sheet: -0.81 (0.47), residues: 125 loop : -0.83 (0.39), residues: 272 ********************** 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 152 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 150 average time/residue: 0.7994 time to fit residues: 124.7331 Evaluate side-chains 147 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0402 time to fit residues: 0.6057 ------------------------------------------------------------------------------- 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: 0.5980 chunk 1 optimal weight: 0.0970 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.0040 chunk 26 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 overall best weight: 0.1568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.093005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.080900 restraints weight = 7357.139| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.00 r_work: 0.3281 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3432 Z= 0.235 Angle : 0.899 12.984 4673 Z= 0.420 Chirality : 0.049 0.221 515 Planarity : 0.006 0.052 598 Dihedral : 5.436 22.688 465 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.41 % Allowed : 41.29 % Favored : 56.30 % 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: -1.57 (0.41), residues: 422 helix: -3.57 (0.86), residues: 25 sheet: -0.85 (0.47), residues: 125 loop : -0.85 (0.39), residues: 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.47 seconds wall clock time: 50 minutes 57.61 seconds (3057.61 seconds total)