Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 19:40:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/07_2023/7zh0_14716.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/07_2023/7zh0_14716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/07_2023/7zh0_14716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/07_2023/7zh0_14716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/07_2023/7zh0_14716.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/07_2023/7zh0_14716.pdb" } resolution = 3.2 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= 0.001 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 22 5.16 5 C 2557 2.51 5 N 640 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 3869 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3869 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 23, 'TRANS': 471} Chain breaks: 3 Time building chain proxies: 2.43, per 1000 atoms: 0.63 Number of scatterers: 3869 At special positions: 0 Unit cell: (102.3, 63.36, 75.9, 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 22 16.00 O 650 8.00 N 640 7.00 C 2557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 691.3 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 80.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.620A pdb=" N THR A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 42 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.162A pdb=" N ALA A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.614A pdb=" N TRP A 152 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 179 removed outlier: 3.835A pdb=" N THR A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.629A pdb=" N ILE A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 234 removed outlier: 3.970A pdb=" N GLY A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.776A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.575A pdb=" N VAL A 288 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.577A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.641A pdb=" N VAL A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 373 removed outlier: 3.655A pdb=" N GLY A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 389 through 405 removed outlier: 4.637A pdb=" N GLY A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 426 Processing helix chain 'A' and resid 433 through 461 removed outlier: 4.268A pdb=" N THR A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 471 through 495 Proline residue: A 485 - end of helix removed outlier: 3.669A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.859A pdb=" N ASP A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 93 262 hydrogen bonds defined for protein. 768 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: 1.07 Time building geometry restraints manager: 1.67 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: 1196 1.34 - 1.46: 633 1.46 - 1.57: 2106 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3965 Sorted by residual: bond pdb=" N PHE A 450 " pdb=" CA PHE A 450 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.35e+00 bond pdb=" N MET A 448 " pdb=" CA MET A 448 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.10e+00 bond pdb=" N GLU A 451 " pdb=" CA GLU A 451 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.96e+00 bond pdb=" N ALA A 449 " pdb=" CA ALA A 449 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.67e+00 bond pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.24e+00 ... (remaining 3960 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.81: 119 106.81 - 113.61: 2168 113.61 - 120.41: 1555 120.41 - 127.21: 1504 127.21 - 134.01: 51 Bond angle restraints: 5397 Sorted by residual: angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.28 107.52 3.76 1.09e+00 8.42e-01 1.19e+01 angle pdb=" C VAL A 470 " pdb=" N SER A 471 " pdb=" CA SER A 471 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" N VAL A 529 " pdb=" CA VAL A 529 " pdb=" C VAL A 529 " ideal model delta sigma weight residual 112.80 109.18 3.62 1.15e+00 7.56e-01 9.90e+00 angle pdb=" C GLU A 13 " pdb=" CA GLU A 13 " pdb=" CB GLU A 13 " ideal model delta sigma weight residual 110.42 116.48 -6.06 1.99e+00 2.53e-01 9.27e+00 angle pdb=" C THR A 297 " pdb=" N ARG A 298 " pdb=" CA ARG A 298 " ideal model delta sigma weight residual 123.91 128.84 -4.93 1.66e+00 3.63e-01 8.82e+00 ... (remaining 5392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 2089 17.90 - 35.79: 161 35.79 - 53.69: 39 53.69 - 71.58: 5 71.58 - 89.48: 4 Dihedral angle restraints: 2298 sinusoidal: 895 harmonic: 1403 Sorted by residual: dihedral pdb=" CA VAL A 532 " pdb=" C VAL A 532 " pdb=" N GLU A 533 " pdb=" CA GLU A 533 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.92e+00 dihedral pdb=" N PHE A 450 " pdb=" CA PHE A 450 " pdb=" CB PHE A 450 " pdb=" CG PHE A 450 " ideal model delta sinusoidal sigma weight residual -60.00 -118.37 58.37 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET A 448 " pdb=" CG MET A 448 " pdb=" SD MET A 448 " pdb=" CE MET A 448 " ideal model delta sinusoidal sigma weight residual 60.00 1.88 58.12 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 427 0.038 - 0.076: 149 0.076 - 0.114: 46 0.114 - 0.151: 3 0.151 - 0.189: 4 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA PHE A 450 " pdb=" N PHE A 450 " pdb=" C PHE A 450 " pdb=" CB PHE A 450 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA MET A 448 " pdb=" N MET A 448 " pdb=" C MET A 448 " pdb=" CB MET A 448 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CB ILE A 523 " pdb=" CA ILE A 523 " pdb=" CG1 ILE A 523 " pdb=" CG2 ILE A 523 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 626 not shown) Planarity restraints: 669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 291 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 292 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 519 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C GLU A 519 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU A 519 " -0.012 2.00e-02 2.50e+03 pdb=" N THR A 520 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 131 " 0.010 2.00e-02 2.50e+03 9.61e-03 2.31e+00 pdb=" CG TRP A 131 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 131 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 131 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 131 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 131 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 131 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 131 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 131 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 131 " 0.000 2.00e-02 2.50e+03 ... (remaining 666 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 240 2.73 - 3.27: 4304 3.27 - 3.82: 6583 3.82 - 4.36: 7315 4.36 - 4.90: 12549 Nonbonded interactions: 30991 Sorted by model distance: nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.191 2.440 nonbonded pdb=" O CYS A 189 " pdb=" OG SER A 278 " model vdw 2.244 2.440 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.254 2.520 nonbonded pdb=" N ARG A 406 " pdb=" OE2 GLU A 519 " model vdw 2.293 2.520 nonbonded pdb=" NE ARG A 178 " pdb=" OD1 ASN A 335 " model vdw 2.296 2.520 ... (remaining 30986 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: 2.350 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: 8.850 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.100 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 0.035 3965 Z= 0.250 Angle : 0.719 6.530 5397 Z= 0.394 Chirality : 0.043 0.189 629 Planarity : 0.005 0.082 669 Dihedral : 13.972 89.476 1394 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 0.24 % 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 (0.39), residues: 487 helix: 1.50 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.47 (0.52), residues: 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.449 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1676 time to fit residues: 17.0809 Evaluate side-chains 55 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.0010 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3965 Z= 0.219 Angle : 0.624 5.867 5397 Z= 0.319 Chirality : 0.040 0.135 629 Planarity : 0.005 0.066 669 Dihedral : 4.394 16.475 536 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 1.96 % 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: 1.39 (0.39), residues: 487 helix: 1.83 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.46 (0.52), residues: 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.440 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 74 average time/residue: 0.1366 time to fit residues: 13.0758 Evaluate side-chains 62 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0490 time to fit residues: 1.0888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 0.0270 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 0.0050 chunk 33 optimal weight: 2.9990 overall best weight: 0.3252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3965 Z= 0.179 Angle : 0.588 6.785 5397 Z= 0.299 Chirality : 0.039 0.130 629 Planarity : 0.005 0.056 669 Dihedral : 4.188 16.894 536 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 1.22 % 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: 1.48 (0.39), residues: 487 helix: 1.88 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.34 (0.48), residues: 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.417 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 79 average time/residue: 0.1301 time to fit residues: 13.3508 Evaluate side-chains 63 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0377 time to fit residues: 0.6319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.7444 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3965 Z= 0.197 Angle : 0.594 7.968 5397 Z= 0.306 Chirality : 0.040 0.167 629 Planarity : 0.005 0.055 669 Dihedral : 4.181 15.734 536 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 2.44 % 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: 1.49 (0.39), residues: 487 helix: 1.85 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -1.33 (0.49), residues: 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.479 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.1371 time to fit residues: 13.8487 Evaluate side-chains 68 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0462 time to fit residues: 1.2286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3965 Z= 0.187 Angle : 0.588 8.177 5397 Z= 0.299 Chirality : 0.039 0.139 629 Planarity : 0.005 0.052 669 Dihedral : 4.162 15.982 536 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 2.20 % 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: 1.41 (0.39), residues: 487 helix: 1.78 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -1.31 (0.49), residues: 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.447 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 73 average time/residue: 0.1496 time to fit residues: 13.8913 Evaluate side-chains 62 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0496 time to fit residues: 0.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3965 Z= 0.247 Angle : 0.632 8.353 5397 Z= 0.325 Chirality : 0.042 0.175 629 Planarity : 0.005 0.051 669 Dihedral : 4.336 16.062 536 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 1.47 % 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: 1.27 (0.39), residues: 487 helix: 1.67 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.22 (0.49), residues: 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.470 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.1281 time to fit residues: 12.0006 Evaluate side-chains 67 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0422 time to fit residues: 0.9069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3965 Z= 0.198 Angle : 0.613 11.096 5397 Z= 0.310 Chirality : 0.040 0.131 629 Planarity : 0.005 0.051 669 Dihedral : 4.252 16.068 536 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 1.47 % 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: 1.23 (0.39), residues: 487 helix: 1.60 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.19 (0.50), residues: 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.460 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 68 average time/residue: 0.1531 time to fit residues: 13.3193 Evaluate side-chains 66 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0404 time to fit residues: 0.7606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.0170 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3965 Z= 0.197 Angle : 0.616 11.673 5397 Z= 0.312 Chirality : 0.040 0.158 629 Planarity : 0.005 0.052 669 Dihedral : 4.271 15.401 536 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 0.49 % 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 (0.38), residues: 487 helix: 1.56 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.19 (0.49), residues: 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.446 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.1539 time to fit residues: 13.4968 Evaluate side-chains 63 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0704 time to fit residues: 0.7014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.0070 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3965 Z= 0.192 Angle : 0.627 11.875 5397 Z= 0.317 Chirality : 0.039 0.152 629 Planarity : 0.005 0.051 669 Dihedral : 4.237 15.117 536 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.24 % 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: 1.23 (0.38), residues: 487 helix: 1.65 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.21 (0.48), residues: 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.404 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.1314 time to fit residues: 11.9076 Evaluate side-chains 62 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3965 Z= 0.226 Angle : 0.644 11.824 5397 Z= 0.327 Chirality : 0.041 0.179 629 Planarity : 0.005 0.051 669 Dihedral : 4.344 16.757 536 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.46 % Rotamer Outliers : 0.24 % 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: 1.06 (0.38), residues: 487 helix: 1.45 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.17 (0.50), residues: 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.445 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.1516 time to fit residues: 12.7741 Evaluate side-chains 61 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0663 time to fit residues: 0.6659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.141024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.121232 restraints weight = 6720.230| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.07 r_work: 0.3684 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3965 Z= 0.224 Angle : 0.644 12.066 5397 Z= 0.327 Chirality : 0.041 0.174 629 Planarity : 0.005 0.052 669 Dihedral : 4.345 15.851 536 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.54 % Favored : 94.25 % Rotamer Outliers : 0.24 % 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: 1.04 (0.38), residues: 487 helix: 1.44 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.19 (0.50), residues: 140 =============================================================================== Job complete usr+sys time: 1304.50 seconds wall clock time: 24 minutes 16.40 seconds (1456.40 seconds total)