Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 00:18:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/04_2023/7wb5_32395.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/04_2023/7wb5_32395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/04_2023/7wb5_32395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/04_2023/7wb5_32395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/04_2023/7wb5_32395.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/04_2023/7wb5_32395.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 15 5.16 5 C 2077 2.51 5 N 533 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 65": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 364": "OD1" <-> "OD2" Residue "R TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 389": "OD1" <-> "OD2" Residue "R GLU 406": "OE1" <-> "OE2" Residue "R ARG 408": "NH1" <-> "NH2" Residue "R TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 471": "OE1" <-> "OE2" Residue "R TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3256 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.33, per 1000 atoms: 0.72 Number of scatterers: 3256 At special positions: 0 Unit cell: (72.36, 88.56, 72.36, 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 15 16.00 O 631 8.00 N 533 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 457.2 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 12 sheets defined 4.4% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 364 through 370 removed outlier: 4.598A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.682A pdb=" N LYS H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.906A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.533A pdb=" N TRP H 50 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.846A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.595A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.572A pdb=" N GLN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.884A pdb=" N ILE R 434 " --> pdb=" O VAL R 511 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS R 432 " --> pdb=" O LEU R 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474 73 hydrogen bonds defined for protein. 171 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: 0.80 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 734 1.33 - 1.45: 857 1.45 - 1.57: 1735 1.57 - 1.69: 1 1.69 - 1.82: 18 Bond restraints: 3345 Sorted by residual: bond pdb=" CA SER R 438 " pdb=" CB SER R 438 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.35e-02 5.49e+03 1.53e+01 bond pdb=" CA SER R 349 " pdb=" CB SER R 349 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.64e-02 3.72e+03 1.43e+01 bond pdb=" N LEU R 452 " pdb=" CA LEU R 452 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" N VAL R 433 " pdb=" CA VAL R 433 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N LYS R 378 " pdb=" CA LYS R 378 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 ... (remaining 3340 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.46: 54 104.46 - 112.01: 1454 112.01 - 119.57: 1347 119.57 - 127.13: 1665 127.13 - 134.69: 28 Bond angle restraints: 4548 Sorted by residual: angle pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA TRP R 436 " pdb=" CB TRP R 436 " pdb=" CG TRP R 436 " ideal model delta sigma weight residual 113.60 123.83 -10.23 1.90e+00 2.77e-01 2.90e+01 angle pdb=" CA PHE R 400 " pdb=" CB PHE R 400 " pdb=" CG PHE R 400 " ideal model delta sigma weight residual 113.80 118.30 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N PRO L 80 " pdb=" CD PRO L 80 " pdb=" CG PRO L 80 " ideal model delta sigma weight residual 103.20 96.90 6.30 1.50e+00 4.44e-01 1.77e+01 angle pdb=" N LEU R 387 " pdb=" CA LEU R 387 " pdb=" C LEU R 387 " ideal model delta sigma weight residual 114.75 109.56 5.19 1.26e+00 6.30e-01 1.69e+01 ... (remaining 4543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 1605 16.17 - 32.35: 206 32.35 - 48.52: 70 48.52 - 64.70: 33 64.70 - 80.87: 6 Dihedral angle restraints: 1920 sinusoidal: 740 harmonic: 1180 Sorted by residual: dihedral pdb=" CA VAL L 29 " pdb=" C VAL L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta harmonic sigma weight residual 180.00 -139.90 -40.10 0 5.00e+00 4.00e-02 6.43e+01 dihedral pdb=" CA PHE H 106 " pdb=" C PHE H 106 " pdb=" N ASP H 107 " pdb=" CA ASP H 107 " ideal model delta harmonic sigma weight residual 180.00 -146.68 -33.32 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.78 -43.78 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 1917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 417 0.119 - 0.238: 63 0.238 - 0.356: 5 0.356 - 0.475: 0 0.475 - 0.593: 2 Chirality restraints: 487 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.29e+01 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.81e+00 ... (remaining 484 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.304 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" C7 NAG A 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.009 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.453 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.292 2.00e-02 2.50e+03 2.51e-01 7.91e+02 pdb=" C7 NAG A 1 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.111 5.00e-02 4.00e+02 1.57e-01 3.92e+01 pdb=" N PRO L 80 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.076 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 281 2.73 - 3.27: 3255 3.27 - 3.82: 5356 3.82 - 4.36: 6706 4.36 - 4.90: 11080 Nonbonded interactions: 26678 Sorted by model distance: nonbonded pdb=" O ILE L 21 " pdb=" OG1 THR L 72 " model vdw 2.188 2.440 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.216 2.440 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 113 " model vdw 2.319 2.440 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.405 2.440 nonbonded pdb=" O VAL H 76 " pdb=" OG SER H 77 " model vdw 2.421 2.440 ... (remaining 26673 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 13.060 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.120 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.011 0.132 3345 Z= 0.690 Angle : 1.407 12.925 4548 Z= 0.926 Chirality : 0.090 0.593 487 Planarity : 0.018 0.262 581 Dihedral : 18.471 80.870 1159 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 2.24 % Allowed : 18.16 % Favored : 79.60 % Rotamer Outliers : 14.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.36), residues: 402 helix: -4.22 (0.64), residues: 21 sheet: -3.58 (0.39), residues: 121 loop : -3.14 (0.35), residues: 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 0.404 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 12 residues processed: 150 average time/residue: 0.1819 time to fit residues: 31.9750 Evaluate side-chains 117 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0801 time to fit residues: 1.8050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 3345 Z= 0.292 Angle : 0.822 8.184 4548 Z= 0.423 Chirality : 0.049 0.175 487 Planarity : 0.007 0.082 581 Dihedral : 6.310 37.685 450 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.69 % Favored : 87.81 % Rotamer Outliers : 4.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.36), residues: 402 helix: -3.60 (0.71), residues: 21 sheet: -3.12 (0.43), residues: 112 loop : -3.10 (0.33), residues: 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.383 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 117 average time/residue: 0.1939 time to fit residues: 26.8069 Evaluate side-chains 108 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0444 time to fit residues: 1.5346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.0040 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3345 Z= 0.235 Angle : 0.732 9.682 4548 Z= 0.374 Chirality : 0.047 0.184 487 Planarity : 0.006 0.078 581 Dihedral : 6.025 35.202 450 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.45 % Favored : 89.05 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.37), residues: 402 helix: -3.63 (0.72), residues: 21 sheet: -2.54 (0.48), residues: 104 loop : -2.83 (0.34), residues: 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 0.1913 time to fit residues: 25.0476 Evaluate side-chains 99 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0844 time to fit residues: 1.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 3345 Z= 0.286 Angle : 0.724 8.793 4548 Z= 0.370 Chirality : 0.046 0.184 487 Planarity : 0.007 0.075 581 Dihedral : 5.944 35.631 450 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.70 % Favored : 89.05 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.37), residues: 402 helix: -3.32 (0.84), residues: 19 sheet: -2.57 (0.48), residues: 109 loop : -2.83 (0.33), residues: 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.388 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.2164 time to fit residues: 26.8227 Evaluate side-chains 101 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0352 time to fit residues: 1.0973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 3345 Z= 0.296 Angle : 0.722 8.017 4548 Z= 0.368 Chirality : 0.047 0.179 487 Planarity : 0.006 0.076 581 Dihedral : 5.896 35.868 450 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.45 % Favored : 90.30 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.38), residues: 402 helix: -3.46 (0.78), residues: 19 sheet: -2.57 (0.48), residues: 109 loop : -2.68 (0.34), residues: 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.383 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 104 average time/residue: 0.1990 time to fit residues: 24.1286 Evaluate side-chains 93 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1366 time to fit residues: 1.3637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.0170 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 450 ASN ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3345 Z= 0.233 Angle : 0.708 7.600 4548 Z= 0.364 Chirality : 0.046 0.172 487 Planarity : 0.006 0.077 581 Dihedral : 5.850 33.699 450 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.37), residues: 402 helix: -3.75 (0.69), residues: 19 sheet: -2.48 (0.49), residues: 105 loop : -2.72 (0.33), residues: 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.362 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 100 average time/residue: 0.1661 time to fit residues: 19.9487 Evaluate side-chains 91 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0364 time to fit residues: 0.6631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 ASN ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 3345 Z= 0.302 Angle : 0.744 7.204 4548 Z= 0.383 Chirality : 0.046 0.161 487 Planarity : 0.006 0.074 581 Dihedral : 5.988 35.199 450 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer Outliers : 4.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.37), residues: 402 helix: -3.64 (0.78), residues: 18 sheet: -2.63 (0.47), residues: 111 loop : -2.67 (0.34), residues: 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.384 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 99 average time/residue: 0.1765 time to fit residues: 20.8751 Evaluate side-chains 101 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0352 time to fit residues: 0.9382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 31 optimal weight: 0.3980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.003 0.029 3345 Z= 0.222 Angle : 0.726 8.063 4548 Z= 0.372 Chirality : 0.045 0.178 487 Planarity : 0.006 0.075 581 Dihedral : 5.727 32.708 450 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.37), residues: 402 helix: -3.57 (0.84), residues: 18 sheet: -2.53 (0.46), residues: 111 loop : -2.62 (0.34), residues: 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.395 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 0.1689 time to fit residues: 19.2052 Evaluate side-chains 92 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0374 time to fit residues: 0.7284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 3345 Z= 0.264 Angle : 0.752 7.347 4548 Z= 0.389 Chirality : 0.046 0.184 487 Planarity : 0.006 0.075 581 Dihedral : 5.776 33.249 450 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.38), residues: 402 helix: -3.85 (0.75), residues: 18 sheet: -2.52 (0.47), residues: 111 loop : -2.54 (0.35), residues: 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.385 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.1872 time to fit residues: 21.1999 Evaluate side-chains 94 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0354 time to fit residues: 0.7747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.0050 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 414 GLN ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 3345 Z= 0.256 Angle : 0.742 7.612 4548 Z= 0.385 Chirality : 0.046 0.189 487 Planarity : 0.006 0.074 581 Dihedral : 5.725 32.726 450 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.38), residues: 402 helix: -4.09 (0.71), residues: 20 sheet: -2.66 (0.44), residues: 120 loop : -2.32 (0.36), residues: 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.392 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 0.1739 time to fit residues: 18.1191 Evaluate side-chains 86 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0364 time to fit residues: 0.5881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 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 = 0.3900 r_free = 0.3900 target = 0.148904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124679 restraints weight = 4915.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127611 restraints weight = 3244.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129544 restraints weight = 2434.324| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3345 Z= 0.219 Angle : 0.736 7.871 4548 Z= 0.378 Chirality : 0.045 0.186 487 Planarity : 0.006 0.076 581 Dihedral : 5.613 31.118 450 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.39), residues: 402 helix: -4.06 (0.73), residues: 20 sheet: -2.47 (0.47), residues: 114 loop : -2.28 (0.35), residues: 268 =============================================================================== Job complete usr+sys time: 1394.98 seconds wall clock time: 25 minutes 38.92 seconds (1538.92 seconds total)