Starting phenix.real_space_refine on Mon Sep 23 12:46:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/09_2024/7tz0_26201.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/09_2024/7tz0_26201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/09_2024/7tz0_26201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/09_2024/7tz0_26201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/09_2024/7tz0_26201.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/09_2024/7tz0_26201.cif" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.100 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 12 5.16 5 C 1699 2.51 5 N 453 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2674 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "B" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Time building chain proxies: 2.46, per 1000 atoms: 0.92 Number of scatterers: 2674 At special positions: 0 Unit cell: (58.491, 66.348, 96.903, 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 12 16.00 O 510 8.00 N 453 7.00 C 1699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.60 Conformation dependent library (CDL) restraints added in 323.3 milliseconds 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 632 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 36.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.304A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 16 through 25 removed outlier: 3.542A pdb=" N GLU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.522A pdb=" N LEU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 4.064A pdb=" N TYR B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 93 through 103 removed outlier: 4.008A pdb=" N GLU B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.528A pdb=" N ARG B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.617A pdb=" N VAL B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.599A pdb=" N ASP B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.839A pdb=" N ALA B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 402 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 72 hydrogen bonds defined for protein. 207 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: 0.54 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 889 1.35 - 1.46: 646 1.46 - 1.58: 1184 1.58 - 1.70: 1 1.70 - 1.81: 14 Bond restraints: 2734 Sorted by residual: bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.13e+00 bond pdb=" CB PRO B 50 " pdb=" CG PRO B 50 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.47e+00 bond pdb=" CB LYS A 458 " pdb=" CG LYS A 458 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.11e-01 bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.503 1.533 -0.030 3.40e-02 8.65e+02 8.03e-01 bond pdb=" CB ARG B 31 " pdb=" CG ARG B 31 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.69e-01 ... (remaining 2729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 3639 1.87 - 3.75: 64 3.75 - 5.62: 9 5.62 - 7.50: 2 7.50 - 9.37: 1 Bond angle restraints: 3715 Sorted by residual: angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 113.42 108.54 4.88 1.17e+00 7.31e-01 1.74e+01 angle pdb=" CA PRO B 50 " pdb=" N PRO B 50 " pdb=" CD PRO B 50 " ideal model delta sigma weight residual 112.00 107.42 4.58 1.40e+00 5.10e-01 1.07e+01 angle pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " ideal model delta sigma weight residual 116.30 125.67 -9.37 3.50e+00 8.16e-02 7.17e+00 angle pdb=" CA LYS A 458 " pdb=" CB LYS A 458 " pdb=" CG LYS A 458 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.14e+00 ... (remaining 3710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 1429 14.80 - 29.59: 143 29.59 - 44.39: 32 44.39 - 59.18: 8 59.18 - 73.98: 2 Dihedral angle restraints: 1614 sinusoidal: 619 harmonic: 995 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 19.02 73.98 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -144.38 58.38 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 46.65 46.35 1 1.00e+01 1.00e-02 2.97e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 223 0.028 - 0.056: 115 0.056 - 0.084: 45 0.084 - 0.112: 19 0.112 - 0.140: 6 Chirality restraints: 408 Sorted by residual: chirality pdb=" CA PRO B 50 " pdb=" N PRO B 50 " pdb=" C PRO B 50 " pdb=" CB PRO B 50 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA PRO A 491 " pdb=" N PRO A 491 " pdb=" C PRO A 491 " pdb=" CB PRO A 491 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL A 382 " pdb=" N VAL A 382 " pdb=" C VAL A 382 " pdb=" CB VAL A 382 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 405 not shown) Planarity restraints: 489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A 384 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 49 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO B 50 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 360 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C ASN A 360 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 360 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 361 " -0.012 2.00e-02 2.50e+03 ... (remaining 486 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 715 2.79 - 3.32: 2669 3.32 - 3.85: 4201 3.85 - 4.37: 4974 4.37 - 4.90: 7820 Nonbonded interactions: 20379 Sorted by model distance: nonbonded pdb=" OG1 THR A 415 " pdb=" OD2 ASP A 420 " model vdw 2.265 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.271 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 2.277 3.120 nonbonded pdb=" NH1 ARG A 357 " pdb=" O ILE A 358 " model vdw 2.281 3.120 nonbonded pdb=" OG1 THR B 82 " pdb=" ND1 HIS B 85 " model vdw 2.306 3.120 ... (remaining 20374 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.090 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.480 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 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 : 0.003 0.113 2734 Z= 0.226 Angle : 0.624 9.374 3715 Z= 0.330 Chirality : 0.041 0.140 408 Planarity : 0.007 0.110 489 Dihedral : 12.380 69.766 970 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.42), residues: 343 helix: -0.69 (0.47), residues: 106 sheet: -1.48 (1.07), residues: 24 loop : -1.37 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.004 0.001 HIS B 52 PHE 0.032 0.001 PHE A 429 TYR 0.012 0.001 TYR A 495 ARG 0.004 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8385 (mp) cc_final: 0.7934 (mp) REVERT: A 498 GLN cc_start: 0.8587 (mp10) cc_final: 0.8268 (mp10) REVERT: B 66 LEU cc_start: 0.8491 (mt) cc_final: 0.8260 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1370 time to fit residues: 13.4424 Evaluate side-chains 72 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 30.0000 chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2734 Z= 0.167 Angle : 0.573 6.468 3715 Z= 0.291 Chirality : 0.043 0.137 408 Planarity : 0.005 0.060 489 Dihedral : 4.598 18.322 376 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: -1.65 (0.42), residues: 343 helix: -0.60 (0.45), residues: 113 sheet: -1.17 (0.90), residues: 30 loop : -1.38 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 353 HIS 0.006 0.002 HIS B 85 PHE 0.009 0.001 PHE A 490 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7949 (mt0) cc_final: 0.7383 (mt0) REVERT: A 418 ILE cc_start: 0.8234 (mp) cc_final: 0.7800 (mp) REVERT: A 429 PHE cc_start: 0.8112 (t80) cc_final: 0.7621 (t80) REVERT: A 442 ASP cc_start: 0.9045 (p0) cc_final: 0.8835 (p0) REVERT: A 498 GLN cc_start: 0.8618 (mp10) cc_final: 0.8287 (mp10) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1128 time to fit residues: 11.6439 Evaluate side-chains 73 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 40.0000 chunk 33 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 422 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 2734 Z= 0.263 Angle : 0.712 11.845 3715 Z= 0.356 Chirality : 0.046 0.167 408 Planarity : 0.005 0.053 489 Dihedral : 5.619 20.191 376 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.35 % Allowed : 5.63 % Favored : 94.01 % 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: -2.10 (0.41), residues: 343 helix: -0.89 (0.43), residues: 115 sheet: -1.70 (0.88), residues: 30 loop : -1.67 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 353 HIS 0.003 0.001 HIS B 52 PHE 0.020 0.002 PHE A 490 TYR 0.014 0.002 TYR A 380 ARG 0.007 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.303 Fit side-chains REVERT: A 374 PHE cc_start: 0.7483 (m-10) cc_final: 0.7188 (m-10) REVERT: A 418 ILE cc_start: 0.8367 (mp) cc_final: 0.7941 (mp) REVERT: A 429 PHE cc_start: 0.8169 (t80) cc_final: 0.7629 (t80) REVERT: A 442 ASP cc_start: 0.9048 (p0) cc_final: 0.8833 (p0) REVERT: A 498 GLN cc_start: 0.8164 (mp10) cc_final: 0.7830 (mp10) REVERT: B 112 ASN cc_start: 0.7759 (t0) cc_final: 0.7312 (t0) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1239 time to fit residues: 12.9834 Evaluate side-chains 70 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.0470 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 0.0270 chunk 20 optimal weight: 0.0870 chunk 31 optimal weight: 40.0000 chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN B 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2734 Z= 0.133 Angle : 0.598 8.497 3715 Z= 0.293 Chirality : 0.043 0.141 408 Planarity : 0.005 0.052 489 Dihedral : 4.683 18.028 376 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.35 % Allowed : 2.82 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.42), residues: 343 helix: -0.33 (0.47), residues: 115 sheet: -1.85 (0.84), residues: 30 loop : -1.39 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.005 0.001 HIS B 85 PHE 0.007 0.001 PHE A 464 TYR 0.012 0.001 TYR A 380 ARG 0.002 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.308 Fit side-chains REVERT: A 354 ASN cc_start: 0.8734 (m-40) cc_final: 0.8512 (m-40) REVERT: A 394 ASN cc_start: 0.7784 (t0) cc_final: 0.7573 (t0) REVERT: A 409 GLN cc_start: 0.8057 (mt0) cc_final: 0.7467 (mt0) REVERT: A 418 ILE cc_start: 0.8403 (mp) cc_final: 0.7960 (mp) REVERT: A 429 PHE cc_start: 0.8198 (t80) cc_final: 0.7651 (t80) REVERT: A 442 ASP cc_start: 0.8976 (p0) cc_final: 0.8759 (p0) REVERT: A 498 GLN cc_start: 0.8447 (mp10) cc_final: 0.8082 (mp10) REVERT: B 155 ASP cc_start: 0.6999 (m-30) cc_final: 0.6789 (m-30) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1279 time to fit residues: 13.2619 Evaluate side-chains 70 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.0010 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 29 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2734 Z= 0.165 Angle : 0.602 8.762 3715 Z= 0.294 Chirality : 0.042 0.134 408 Planarity : 0.005 0.050 489 Dihedral : 4.795 19.879 376 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -1.71 (0.42), residues: 343 helix: -0.38 (0.45), residues: 121 sheet: -2.32 (0.87), residues: 25 loop : -1.47 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.004 0.001 HIS B 52 PHE 0.011 0.001 PHE A 490 TYR 0.013 0.001 TYR A 380 ARG 0.003 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8989 (t0) cc_final: 0.8777 (t0) REVERT: A 418 ILE cc_start: 0.8386 (mp) cc_final: 0.7896 (mp) REVERT: A 429 PHE cc_start: 0.8231 (t80) cc_final: 0.7671 (t80) REVERT: A 442 ASP cc_start: 0.9014 (p0) cc_final: 0.8798 (p0) REVERT: A 495 TYR cc_start: 0.7817 (m-80) cc_final: 0.7477 (m-80) REVERT: A 498 GLN cc_start: 0.8427 (mp10) cc_final: 0.8071 (mp10) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1200 time to fit residues: 12.1364 Evaluate side-chains 73 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 40.0000 chunk 3 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 36 ASN B 112 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2734 Z= 0.201 Angle : 0.648 10.560 3715 Z= 0.317 Chirality : 0.043 0.138 408 Planarity : 0.005 0.048 489 Dihedral : 5.113 18.976 376 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.70 % Allowed : 1.76 % Favored : 97.54 % 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: -1.66 (0.43), residues: 343 helix: -0.17 (0.47), residues: 109 sheet: -1.70 (0.86), residues: 31 loop : -1.56 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.015 0.002 PHE A 490 TYR 0.011 0.002 TYR A 396 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.262 Fit side-chains REVERT: A 364 ASP cc_start: 0.8963 (t0) cc_final: 0.8728 (t0) REVERT: A 394 ASN cc_start: 0.7797 (t0) cc_final: 0.7578 (t0) REVERT: A 418 ILE cc_start: 0.8418 (mp) cc_final: 0.7942 (mp) REVERT: A 429 PHE cc_start: 0.8295 (t80) cc_final: 0.7724 (t80) REVERT: A 442 ASP cc_start: 0.9000 (p0) cc_final: 0.8746 (p0) REVERT: A 498 GLN cc_start: 0.8221 (mp10) cc_final: 0.7851 (mp10) outliers start: 2 outliers final: 1 residues processed: 78 average time/residue: 0.1190 time to fit residues: 11.3417 Evaluate side-chains 68 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2734 Z= 0.181 Angle : 0.638 10.675 3715 Z= 0.311 Chirality : 0.043 0.137 408 Planarity : 0.005 0.048 489 Dihedral : 4.983 19.226 376 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.43), residues: 343 helix: -0.47 (0.44), residues: 121 sheet: -1.83 (0.82), residues: 31 loop : -1.48 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 79 HIS 0.003 0.001 HIS B 85 PHE 0.020 0.002 PHE A 347 TYR 0.008 0.001 TYR A 495 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.285 Fit side-chains REVERT: A 394 ASN cc_start: 0.7930 (t0) cc_final: 0.7718 (t0) REVERT: A 418 ILE cc_start: 0.8436 (mp) cc_final: 0.7933 (mp) REVERT: A 429 PHE cc_start: 0.8288 (t80) cc_final: 0.7709 (t80) REVERT: A 442 ASP cc_start: 0.8957 (p0) cc_final: 0.8698 (p0) REVERT: A 495 TYR cc_start: 0.7820 (m-80) cc_final: 0.7550 (m-80) REVERT: A 498 GLN cc_start: 0.8210 (mp10) cc_final: 0.7870 (mp10) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1255 time to fit residues: 12.2112 Evaluate side-chains 66 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.0370 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 112 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2734 Z= 0.213 Angle : 0.671 12.305 3715 Z= 0.329 Chirality : 0.044 0.140 408 Planarity : 0.005 0.048 489 Dihedral : 5.253 19.253 376 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.70 % Allowed : 1.06 % Favored : 98.24 % 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: -1.78 (0.44), residues: 343 helix: -0.28 (0.46), residues: 113 sheet: -1.98 (0.83), residues: 33 loop : -1.60 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.004 0.001 HIS B 52 PHE 0.017 0.002 PHE A 347 TYR 0.008 0.001 TYR A 396 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.277 Fit side-chains REVERT: A 364 ASP cc_start: 0.8855 (t0) cc_final: 0.8596 (t0) REVERT: A 394 ASN cc_start: 0.7968 (t0) cc_final: 0.7768 (t0) REVERT: A 418 ILE cc_start: 0.8435 (mp) cc_final: 0.7982 (mp) REVERT: A 429 PHE cc_start: 0.8295 (t80) cc_final: 0.7725 (t80) REVERT: A 442 ASP cc_start: 0.8925 (p0) cc_final: 0.8663 (p0) REVERT: A 458 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8267 (tptt) REVERT: A 498 GLN cc_start: 0.8074 (mp10) cc_final: 0.7699 (mp10) outliers start: 2 outliers final: 0 residues processed: 77 average time/residue: 0.1340 time to fit residues: 12.5822 Evaluate side-chains 66 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 422 ASN B 112 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2734 Z= 0.246 Angle : 0.725 15.268 3715 Z= 0.355 Chirality : 0.045 0.150 408 Planarity : 0.005 0.047 489 Dihedral : 5.596 19.628 376 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 1.06 % Allowed : 1.06 % Favored : 97.89 % 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: -2.18 (0.42), residues: 343 helix: -0.61 (0.44), residues: 113 sheet: -2.64 (0.88), residues: 26 loop : -1.82 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.020 0.002 PHE A 347 TYR 0.013 0.002 TYR A 453 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.300 Fit side-chains REVERT: A 364 ASP cc_start: 0.8905 (t0) cc_final: 0.8680 (t0) REVERT: A 418 ILE cc_start: 0.8497 (mp) cc_final: 0.8082 (mp) REVERT: A 429 PHE cc_start: 0.8310 (t80) cc_final: 0.7799 (t80) REVERT: A 495 TYR cc_start: 0.7828 (m-80) cc_final: 0.7612 (m-80) REVERT: A 498 GLN cc_start: 0.7868 (mp10) cc_final: 0.7594 (mp10) REVERT: B 17 LYS cc_start: 0.9023 (mmpt) cc_final: 0.8811 (mmmt) outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 0.1298 time to fit residues: 12.0058 Evaluate side-chains 68 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 21 optimal weight: 0.0010 chunk 28 optimal weight: 0.1980 chunk 8 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 0.0670 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2734 Z= 0.139 Angle : 0.625 10.795 3715 Z= 0.306 Chirality : 0.043 0.133 408 Planarity : 0.005 0.048 489 Dihedral : 4.853 18.973 376 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.87 (0.43), residues: 343 helix: -0.33 (0.45), residues: 117 sheet: -2.99 (0.80), residues: 26 loop : -1.57 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.002 0.001 HIS B 85 PHE 0.016 0.001 PHE A 347 TYR 0.015 0.001 TYR A 396 ARG 0.006 0.001 ARG A 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.281 Fit side-chains REVERT: A 350 VAL cc_start: 0.8953 (p) cc_final: 0.8738 (m) REVERT: A 418 ILE cc_start: 0.8470 (mp) cc_final: 0.7939 (mp) REVERT: A 429 PHE cc_start: 0.8233 (t80) cc_final: 0.7658 (t80) REVERT: A 442 ASP cc_start: 0.8836 (p0) cc_final: 0.8477 (p0) REVERT: A 495 TYR cc_start: 0.7911 (m-80) cc_final: 0.7695 (m-80) REVERT: A 498 GLN cc_start: 0.8191 (mp10) cc_final: 0.7877 (mp10) REVERT: B 17 LYS cc_start: 0.8983 (mmpt) cc_final: 0.8728 (mmmt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1324 time to fit residues: 12.1643 Evaluate side-chains 72 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 9.9990 chunk 1 optimal weight: 0.0050 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 overall best weight: 3.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 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 = 0.4382 r_free = 0.4382 target = 0.187265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.161003 restraints weight = 7072.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.165376 restraints weight = 4855.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.168548 restraints weight = 3540.970| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2734 Z= 0.177 Angle : 0.628 11.331 3715 Z= 0.308 Chirality : 0.042 0.136 408 Planarity : 0.005 0.049 489 Dihedral : 4.842 20.428 376 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.85 (0.43), residues: 343 helix: -0.37 (0.45), residues: 118 sheet: -1.95 (0.84), residues: 33 loop : -1.67 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.003 0.001 HIS B 85 PHE 0.016 0.002 PHE A 347 TYR 0.013 0.001 TYR A 495 ARG 0.008 0.001 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 940.82 seconds wall clock time: 17 minutes 25.77 seconds (1045.77 seconds total)