Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 17:34:29 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/12_2021/7kdt_22829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/12_2021/7kdt_22829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/12_2021/7kdt_22829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/12_2021/7kdt_22829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/12_2021/7kdt_22829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdt_22829/12_2021/7kdt_22829.pdb" } resolution = 3.05 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= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 8064 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7444 Classifications: {'peptide': 467} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 454} Chain breaks: 1 Chain: "B" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 620 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Time building chain proxies: 4.18, per 1000 atoms: 0.52 Number of scatterers: 8064 At special positions: 0 Unit cell: (57.546, 70.89, 115.926, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 769 8.00 N 683 7.00 C 2543 6.00 H 4042 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 7.12 Conformation dependent library (CDL) restraints added in 651.3 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 109 through 127 removed outlier: 4.286A pdb=" N ALA A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.708A pdb=" N ALA A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 221 through 245 removed outlier: 3.571A pdb=" N GLU A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 299 through 307 removed outlier: 4.360A pdb=" N GLN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.501A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 343 removed outlier: 6.115A pdb=" N GLU A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Proline residue: A 350 - end of helix removed outlier: 3.595A pdb=" N VAL A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 380 Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.624A pdb=" N ALA A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.809A pdb=" N TYR A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.521A pdb=" N ALA A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 452 removed outlier: 3.653A pdb=" N GLN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 472 removed outlier: 3.816A pdb=" N GLU A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.514A pdb=" N GLU A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 521 removed outlier: 4.136A pdb=" N TYR A 513 " --> pdb=" O ASN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 removed outlier: 3.881A pdb=" N GLU A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 558 Processing helix chain 'A' and resid 560 through 573 Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.688A pdb=" N HIS A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 599 " --> pdb=" O THR A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 69 removed outlier: 4.876A pdb=" N SER B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 290 hydrogen bonds defined for protein. 858 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: 2.75 Time building geometry restraints manager: 7.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 1022 1.06 - 1.25: 3587 1.25 - 1.44: 1110 1.44 - 1.63: 2367 1.63 - 1.82: 42 Bond restraints: 8128 Sorted by residual: bond pdb=" C GLN A 115 " pdb=" O GLN A 115 " ideal model delta sigma weight residual 1.236 1.141 0.095 1.15e-02 7.56e+03 6.85e+01 bond pdb=" N GLU A 549 " pdb=" H GLU A 549 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD1 TYR A 479 " pdb=" HD1 TYR A 479 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD1 PHE A 390 " pdb=" HD1 PHE A 390 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD1 TYR A 304 " pdb=" HD1 TYR A 304 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 8123 not shown) Histogram of bond angle deviations from ideal: 95.77 - 103.49: 54 103.49 - 111.21: 8481 111.21 - 118.93: 2963 118.93 - 126.65: 3194 126.65 - 134.37: 38 Bond angle restraints: 14730 Sorted by residual: angle pdb=" CA GLN A 115 " pdb=" C GLN A 115 " pdb=" O GLN A 115 " ideal model delta sigma weight residual 120.82 114.53 6.29 1.05e+00 9.07e-01 3.58e+01 angle pdb=" CA GLN A 132 " pdb=" C GLN A 132 " pdb=" O GLN A 132 " ideal model delta sigma weight residual 120.42 114.45 5.97 1.06e+00 8.90e-01 3.18e+01 angle pdb=" N GLN A 416 " pdb=" CA GLN A 416 " pdb=" C GLN A 416 " ideal model delta sigma weight residual 109.62 102.09 7.53 1.50e+00 4.44e-01 2.52e+01 angle pdb=" C LYS A 516 " pdb=" N GLY A 517 " pdb=" CA GLY A 517 " ideal model delta sigma weight residual 119.94 125.39 -5.45 1.09e+00 8.42e-01 2.50e+01 angle pdb=" CA LYS A 349 " pdb=" C LYS A 349 " pdb=" O LYS A 349 " ideal model delta sigma weight residual 118.33 113.80 4.53 9.20e-01 1.18e+00 2.43e+01 ... (remaining 14725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3028 17.70 - 35.41: 160 35.41 - 53.11: 26 53.11 - 70.81: 34 70.81 - 88.52: 21 Dihedral angle restraints: 3269 sinusoidal: 1556 harmonic: 1713 Sorted by residual: dihedral pdb=" CA GLU A 320 " pdb=" C GLU A 320 " pdb=" N ILE A 321 " pdb=" CA ILE A 321 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N ARG B 47 " pdb=" CA ARG B 47 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA THR A 451 " pdb=" C THR A 451 " pdb=" N GLY A 452 " pdb=" CA GLY A 452 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 3266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 342 0.063 - 0.127: 181 0.127 - 0.190: 51 0.190 - 0.253: 22 0.253 - 0.316: 6 Chirality restraints: 602 Sorted by residual: chirality pdb=" CA GLU A 308 " pdb=" N GLU A 308 " pdb=" C GLU A 308 " pdb=" CB GLU A 308 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA PHE A 219 " pdb=" N PHE A 219 " pdb=" C PHE A 219 " pdb=" CB PHE A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ARG A 529 " pdb=" N ARG A 529 " pdb=" C ARG A 529 " pdb=" CB ARG A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 599 not shown) Planarity restraints: 1201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 520 " 0.056 2.00e-02 2.50e+03 4.40e-01 2.91e+03 pdb=" CD GLN A 520 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN A 520 " -0.052 2.00e-02 2.50e+03 pdb=" NE2 GLN A 520 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 520 " 0.768 2.00e-02 2.50e+03 pdb="HE22 GLN A 520 " -0.754 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 115 " 0.078 2.00e-02 2.50e+03 4.36e-01 2.85e+03 pdb=" CD GLN A 115 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN A 115 " -0.084 2.00e-02 2.50e+03 pdb=" NE2 GLN A 115 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 115 " -0.753 2.00e-02 2.50e+03 pdb="HE22 GLN A 115 " 0.748 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 220 " 0.119 2.00e-02 2.50e+03 4.33e-01 2.82e+03 pdb=" CD GLN A 220 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 220 " -0.115 2.00e-02 2.50e+03 pdb=" NE2 GLN A 220 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 220 " 0.745 2.00e-02 2.50e+03 pdb="HE22 GLN A 220 " -0.738 2.00e-02 2.50e+03 ... (remaining 1198 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 413 2.20 - 2.80: 15423 2.80 - 3.40: 23181 3.40 - 4.00: 29503 4.00 - 4.60: 44103 Nonbonded interactions: 112623 Sorted by model distance: nonbonded pdb=" OD2 ASP A 267 " pdb=" HG SER A 270 " model vdw 1.603 1.850 nonbonded pdb=" OE1 GLU A 217 " pdb=" HG SER A 224 " model vdw 1.611 1.850 nonbonded pdb=" OD1 ASP A 151 " pdb=" HG SER A 153 " model vdw 1.625 1.850 nonbonded pdb=" O ALA A 483 " pdb=" HG1 THR A 487 " model vdw 1.654 1.850 nonbonded pdb=" OD1 ASN A 509 " pdb=" HG1 THR A 512 " model vdw 1.663 1.850 ... (remaining 112618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 2543 2.51 5 N 683 2.21 5 O 769 1.98 5 H 4042 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Write .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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.170 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 29.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.012 0.095 4086 Z= 0.778 Angle : 1.742 7.528 5493 Z= 1.206 Chirality : 0.088 0.316 602 Planarity : 0.018 0.193 714 Dihedral : 14.556 88.516 1574 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 0.47 % 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: -1.64 (0.32), residues: 499 helix: -0.92 (0.21), residues: 405 sheet: None (None), residues: 0 loop : -0.95 (0.65), residues: 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.3932 time to fit residues: 58.1880 Evaluate side-chains 71 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7997 ------------------------------------------------------------------------------- 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: 0.9980 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 515 HIS A 520 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 4086 Z= 0.216 Angle : 0.592 5.588 5493 Z= 0.325 Chirality : 0.035 0.136 602 Planarity : 0.006 0.120 714 Dihedral : 4.949 23.595 542 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.93 % 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: 1.01 (0.36), residues: 499 helix: 1.02 (0.24), residues: 412 sheet: None (None), residues: 0 loop : -0.70 (0.62), residues: 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 82 average time/residue: 0.2941 time to fit residues: 31.1385 Evaluate side-chains 68 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1078 time to fit residues: 1.3943 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4086 Z= 0.210 Angle : 0.518 4.726 5493 Z= 0.285 Chirality : 0.034 0.120 602 Planarity : 0.005 0.083 714 Dihedral : 4.442 20.635 542 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.93 % 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: 1.59 (0.37), residues: 499 helix: 1.41 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -0.50 (0.68), residues: 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.3249 time to fit residues: 27.7312 Evaluate side-chains 61 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0932 time to fit residues: 1.0358 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4086 Z= 0.174 Angle : 0.478 4.939 5493 Z= 0.260 Chirality : 0.032 0.116 602 Planarity : 0.004 0.062 714 Dihedral : 4.173 19.267 542 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.93 % 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: 2.14 (0.37), residues: 499 helix: 1.80 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -0.41 (0.70), residues: 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.3008 time to fit residues: 27.3326 Evaluate side-chains 63 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1133 time to fit residues: 1.1793 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.7942 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 4086 Z= 0.316 Angle : 0.545 4.368 5493 Z= 0.304 Chirality : 0.036 0.129 602 Planarity : 0.004 0.054 714 Dihedral : 4.375 18.406 542 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.36), residues: 499 helix: 1.49 (0.24), residues: 412 sheet: None (None), residues: 0 loop : -0.67 (0.70), residues: 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 0.3599 time to fit residues: 29.1393 Evaluate side-chains 59 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1001 time to fit residues: 1.0628 ------------------------------------------------------------------------------- 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: 3.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4086 Z= 0.295 Angle : 0.526 4.437 5493 Z= 0.292 Chirality : 0.035 0.125 602 Planarity : 0.004 0.046 714 Dihedral : 4.334 17.963 542 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.36), residues: 499 helix: 1.55 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -0.75 (0.69), residues: 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 65 average time/residue: 0.3226 time to fit residues: 26.9458 Evaluate side-chains 59 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0901 time to fit residues: 1.1423 ------------------------------------------------------------------------------- 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: 0.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7861 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 4086 Z= 0.147 Angle : 0.468 6.845 5493 Z= 0.251 Chirality : 0.032 0.114 602 Planarity : 0.003 0.043 714 Dihedral : 4.004 17.867 542 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 0.47 % 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: 2.51 (0.38), residues: 499 helix: 2.10 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.49 (0.70), residues: 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 63 average time/residue: 0.3150 time to fit residues: 25.5027 Evaluate side-chains 63 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.732 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1024 time to fit residues: 1.2696 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7858 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 4086 Z= 0.156 Angle : 0.472 6.661 5493 Z= 0.251 Chirality : 0.032 0.116 602 Planarity : 0.003 0.037 714 Dihedral : 3.893 17.526 542 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 0.23 % 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: 2.72 (0.38), residues: 499 helix: 2.27 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.53 (0.68), residues: 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.3576 time to fit residues: 26.3015 Evaluate side-chains 57 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1005 time to fit residues: 1.1477 ------------------------------------------------------------------------------- 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: 4.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7866 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4086 Z= 0.167 Angle : 0.470 6.167 5493 Z= 0.251 Chirality : 0.032 0.115 602 Planarity : 0.003 0.037 714 Dihedral : 3.849 17.267 542 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.37), residues: 499 helix: 2.34 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.59 (0.67), residues: 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3396 time to fit residues: 24.7022 Evaluate side-chains 54 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8792 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7880 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4086 Z= 0.183 Angle : 0.479 6.006 5493 Z= 0.255 Chirality : 0.032 0.116 602 Planarity : 0.003 0.035 714 Dihedral : 3.862 17.046 542 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.23 % 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: 2.76 (0.37), residues: 499 helix: 2.33 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.66 (0.66), residues: 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.3813 time to fit residues: 26.6811 Evaluate side-chains 55 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9066 ------------------------------------------------------------------------------- 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: 4.9990 chunk 34 optimal weight: 0.0570 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.156495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132761 restraints weight = 16276.676| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.31 r_work: 0.3773 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work: 0.3733 rms_B_bonded: 2.29 restraints_weight: 0.1250 r_work: 0.3706 rms_B_bonded: 2.65 restraints_weight: 0.0625 r_work: 0.3674 rms_B_bonded: 3.19 restraints_weight: 0.0312 r_work: 0.3634 rms_B_bonded: 3.97 restraints_weight: 0.0156 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 4086 Z= 0.146 Angle : 0.460 5.763 5493 Z= 0.241 Chirality : 0.031 0.114 602 Planarity : 0.003 0.038 714 Dihedral : 3.739 17.079 542 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.38), residues: 499 helix: 2.54 (0.25), residues: 413 sheet: None (None), residues: 0 loop : -0.64 (0.67), residues: 86 =============================================================================== Job complete usr+sys time: 2344.31 seconds wall clock time: 42 minutes 12.55 seconds (2532.55 seconds total)