Starting phenix.real_space_refine on Wed Nov 15 14:55:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/11_2023/8f7a_28899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/11_2023/8f7a_28899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/11_2023/8f7a_28899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/11_2023/8f7a_28899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/11_2023/8f7a_28899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/11_2023/8f7a_28899_updated.pdb" } resolution = 3.78 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5465 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 38 5.16 5 C 4335 2.51 5 N 1119 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 632": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 6742 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5332 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 5327 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 683, 5327 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 5431 Chain: "B" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1410 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'peptide': 169, 'undetermined': 2} Link IDs: {'PTRANS': 6, 'TRANS': 162, None: 2} Not linked: pdbres="PHE B 178 " pdbres=" MG B 301 " Not linked: pdbres=" MG B 301 " pdbres="GTP B 302 " Time building chain proxies: 6.56, per 1000 atoms: 0.97 Number of scatterers: 6742 At special positions: 0 Unit cell: (76.167, 97.092, 104.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 3 15.00 Mg 1 11.99 O 1246 8.00 N 1119 7.00 C 4335 6.00 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 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 2.1 seconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 2 sheets defined 64.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 37 through 52 removed outlier: 5.267A pdb=" N VAL A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 removed outlier: 3.951A pdb=" N GLY A 57 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 58 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 87 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.871A pdb=" N GLU A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.790A pdb=" N TRP A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.071A pdb=" N MET A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 179 through 198 Proline residue: A 183 - end of helix Proline residue: A 187 - end of helix Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 205 through 228 Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 262 through 278 Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 287 through 308 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 350 through 367 removed outlier: 3.708A pdb=" N LYS A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Proline residue: A 358 - end of helix removed outlier: 4.156A pdb=" N TYR A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'A' and resid 444 through 455 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 474 through 480 Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 492 through 507 removed outlier: 4.138A pdb=" N ARG A 504 " --> pdb=" O TRP A 500 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 525 Processing helix chain 'A' and resid 531 through 551 removed outlier: 3.717A pdb=" N LYS A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 558 through 572 Proline residue: A 562 - end of helix removed outlier: 3.517A pdb=" N LEU A 565 " --> pdb=" O PRO A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 593 removed outlier: 4.402A pdb=" N GLU A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 615 removed outlier: 6.028A pdb=" N SER A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 605 " --> pdb=" O MET A 601 " (cutoff:3.500A) Proline residue: A 607 - end of helix Processing helix chain 'A' and resid 620 through 635 removed outlier: 3.677A pdb=" N GLN A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 removed outlier: 4.580A pdb=" N GLY A 641 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Proline residue: A 642 - end of helix removed outlier: 4.885A pdb=" N ILE A 648 " --> pdb=" O MET A 645 " (cutoff:3.500A) Proline residue: A 649 - end of helix removed outlier: 3.632A pdb=" N GLN A 656 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 679 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 693 through 703 Processing helix chain 'A' and resid 707 through 722 removed outlier: 4.112A pdb=" N SER A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 98 through 101 No H-bonds generated for 'chain 'B' and resid 98 through 101' Processing helix chain 'B' and resid 103 through 113 removed outlier: 4.343A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 Processing sheet with id= A, first strand: chain 'B' and resid 11 through 16 removed outlier: 3.715A pdb=" N LEU B 15 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 65 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 67 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 48 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 53 through 56 removed outlier: 4.119A pdb=" N GLY B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2152 1.34 - 1.46: 1293 1.46 - 1.57: 3379 1.57 - 1.69: 5 1.69 - 1.81: 60 Bond restraints: 6889 Sorted by residual: bond pdb=" CA TRP B 66 " pdb=" CB TRP B 66 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.51e-02 4.39e+03 1.77e+00 bond pdb=" CA THR B 137 " pdb=" CB THR B 137 " ideal model delta sigma weight residual 1.534 1.513 0.021 1.78e-02 3.16e+03 1.36e+00 bond pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta sigma weight residual 1.466 1.452 0.015 1.36e-02 5.41e+03 1.16e+00 bond pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 1.528 1.514 0.014 1.33e-02 5.65e+03 1.07e+00 bond pdb=" CB TRP B 66 " pdb=" CG TRP B 66 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 ... (remaining 6884 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.76: 220 106.76 - 113.58: 3974 113.58 - 120.40: 2618 120.40 - 127.22: 2478 127.22 - 134.04: 86 Bond angle restraints: 9376 Sorted by residual: angle pdb=" C THR B 139 " pdb=" N PHE B 140 " pdb=" CA PHE B 140 " ideal model delta sigma weight residual 122.09 116.56 5.53 1.79e+00 3.12e-01 9.53e+00 angle pdb=" N ILE A 237 " pdb=" CA ILE A 237 " pdb=" C ILE A 237 " ideal model delta sigma weight residual 109.34 115.13 -5.79 2.08e+00 2.31e-01 7.74e+00 angle pdb=" N LYS B 136 " pdb=" CA LYS B 136 " pdb=" C LYS B 136 " ideal model delta sigma weight residual 113.01 109.68 3.33 1.20e+00 6.94e-01 7.70e+00 angle pdb=" C1' GTP B 302 " pdb=" O4' GTP B 302 " pdb=" C4' GTP B 302 " ideal model delta sigma weight residual 111.80 103.96 7.84 3.00e+00 1.11e-01 6.83e+00 angle pdb=" C2' GTP B 302 " pdb=" C1' GTP B 302 " pdb=" N9 GTP B 302 " ideal model delta sigma weight residual 109.47 117.16 -7.69 3.00e+00 1.11e-01 6.57e+00 ... (remaining 9371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3730 17.52 - 35.03: 283 35.03 - 52.55: 93 52.55 - 70.06: 26 70.06 - 87.58: 7 Dihedral angle restraints: 4139 sinusoidal: 1631 harmonic: 2508 Sorted by residual: dihedral pdb=" CA ASN B 158 " pdb=" C ASN B 158 " pdb=" N PHE B 159 " pdb=" CA PHE B 159 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 236 " pdb=" C LEU A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ALA A 143 " pdb=" C ALA A 143 " pdb=" N TRP A 144 " pdb=" CA TRP A 144 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 929 0.055 - 0.110: 160 0.110 - 0.165: 11 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1102 Sorted by residual: chirality pdb=" C1' GTP B 302 " pdb=" C2' GTP B 302 " pdb=" N9 GTP B 302 " pdb=" O4' GTP B 302 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2' GTP B 302 " pdb=" C1' GTP B 302 " pdb=" C3' GTP B 302 " pdb=" O2' GTP B 302 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" C3' GTP B 302 " pdb=" C2' GTP B 302 " pdb=" C4' GTP B 302 " pdb=" O3' GTP B 302 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1099 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 144 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 145 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 238 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 239 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 682 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO A 683 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 683 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 683 " 0.020 5.00e-02 4.00e+02 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 2 1.85 - 2.61: 125 2.61 - 3.37: 9963 3.37 - 4.14: 15755 4.14 - 4.90: 29172 Nonbonded interactions: 55017 Sorted by model distance: nonbonded pdb=" OG1 THR B 26 " pdb="MG MG B 301 " model vdw 1.085 2.170 nonbonded pdb="MG MG B 301 " pdb=" O3G GTP B 302 " model vdw 1.776 2.170 nonbonded pdb=" O PHE A 613 " pdb=" OG SER A 617 " model vdw 2.159 2.440 nonbonded pdb=" O PHE A 197 " pdb=" NH1 ARG A 208 " model vdw 2.162 2.520 nonbonded pdb=" OD2 ASP B 93 " pdb=" OG1 THR B 95 " model vdw 2.190 2.440 ... (remaining 55012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 5.990 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 25.390 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 : 0.005 0.046 6889 Z= 0.337 Angle : 0.692 7.842 9376 Z= 0.387 Chirality : 0.041 0.275 1102 Planarity : 0.004 0.042 1177 Dihedral : 15.306 87.575 2501 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 11.80 % Allowed : 9.50 % Favored : 78.70 % 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: -2.21 (0.27), residues: 843 helix: -0.71 (0.21), residues: 545 sheet: -4.45 (0.50), residues: 47 loop : -2.26 (0.38), residues: 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 223 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 20 residues processed: 280 average time/residue: 0.1772 time to fit residues: 65.7799 Evaluate side-chains 164 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 0.779 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.0702 time to fit residues: 3.5671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 374 GLN A 384 GLN A 414 GLN A 434 GLN A 447 HIS A 640 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN A 712 ASN B 147 GLN B 156 ASN B 158 ASN B 175 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6889 Z= 0.219 Angle : 0.743 8.727 9376 Z= 0.375 Chirality : 0.045 0.268 1102 Planarity : 0.005 0.043 1177 Dihedral : 5.828 61.091 915 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.63 % Favored : 95.25 % Rotamer: Outliers : 4.34 % Allowed : 21.03 % Favored : 74.63 % 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: -0.79 (0.29), residues: 843 helix: 0.28 (0.22), residues: 543 sheet: -3.49 (0.65), residues: 40 loop : -1.60 (0.39), residues: 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 183 average time/residue: 0.1592 time to fit residues: 40.6203 Evaluate side-chains 151 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0888 time to fit residues: 2.7435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 64 optimal weight: 0.0050 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 overall best weight: 0.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS A 640 GLN B 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6889 Z= 0.188 Angle : 0.712 10.790 9376 Z= 0.351 Chirality : 0.043 0.177 1102 Planarity : 0.004 0.044 1177 Dihedral : 5.604 56.760 915 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.17 % Allowed : 23.61 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.29), residues: 843 helix: 0.49 (0.23), residues: 539 sheet: -3.85 (0.61), residues: 35 loop : -1.55 (0.38), residues: 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 168 average time/residue: 0.1644 time to fit residues: 37.9910 Evaluate side-chains 138 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0723 time to fit residues: 1.6418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6889 Z= 0.187 Angle : 0.711 9.425 9376 Z= 0.344 Chirality : 0.044 0.211 1102 Planarity : 0.004 0.042 1177 Dihedral : 5.484 56.623 915 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.17 % Allowed : 25.24 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.29), residues: 843 helix: 0.58 (0.23), residues: 528 sheet: -3.27 (0.73), residues: 35 loop : -1.41 (0.38), residues: 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 157 average time/residue: 0.1714 time to fit residues: 36.9079 Evaluate side-chains 141 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0696 time to fit residues: 2.1134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 61 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6889 Z= 0.186 Angle : 0.703 12.365 9376 Z= 0.339 Chirality : 0.043 0.154 1102 Planarity : 0.004 0.042 1177 Dihedral : 5.395 57.224 915 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.63 % Allowed : 24.69 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 843 helix: 0.66 (0.23), residues: 536 sheet: -2.94 (0.67), residues: 46 loop : -1.30 (0.38), residues: 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 149 average time/residue: 0.1600 time to fit residues: 33.3151 Evaluate side-chains 134 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0650 time to fit residues: 1.9220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6889 Z= 0.200 Angle : 0.724 14.124 9376 Z= 0.348 Chirality : 0.043 0.251 1102 Planarity : 0.004 0.042 1177 Dihedral : 5.517 62.674 915 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.36 % Allowed : 25.92 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 843 helix: 0.61 (0.23), residues: 535 sheet: -1.65 (0.76), residues: 39 loop : -1.34 (0.38), residues: 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 143 average time/residue: 0.1612 time to fit residues: 32.7953 Evaluate side-chains 130 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0902 time to fit residues: 1.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.0040 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6889 Z= 0.189 Angle : 0.719 13.866 9376 Z= 0.346 Chirality : 0.044 0.360 1102 Planarity : 0.004 0.043 1177 Dihedral : 5.424 64.719 915 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.49 % Allowed : 26.87 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 843 helix: 0.64 (0.23), residues: 538 sheet: -2.38 (0.70), residues: 49 loop : -1.07 (0.39), residues: 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 137 average time/residue: 0.1668 time to fit residues: 31.9133 Evaluate side-chains 131 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0679 time to fit residues: 1.6184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 64 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6889 Z= 0.178 Angle : 0.725 14.520 9376 Z= 0.345 Chirality : 0.043 0.335 1102 Planarity : 0.004 0.044 1177 Dihedral : 5.394 67.544 915 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.81 % Allowed : 27.14 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.29), residues: 843 helix: 0.70 (0.23), residues: 534 sheet: -2.08 (0.73), residues: 48 loop : -1.10 (0.38), residues: 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 140 average time/residue: 0.1573 time to fit residues: 30.6904 Evaluate side-chains 129 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.732 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0642 time to fit residues: 1.5201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.0270 chunk 76 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS A 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.7543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6889 Z= 0.198 Angle : 0.743 15.682 9376 Z= 0.353 Chirality : 0.045 0.431 1102 Planarity : 0.004 0.044 1177 Dihedral : 5.535 69.515 915 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.68 % Allowed : 27.68 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.29), residues: 843 helix: 0.67 (0.23), residues: 532 sheet: -2.22 (0.68), residues: 52 loop : -0.97 (0.39), residues: 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 130 average time/residue: 0.1528 time to fit residues: 28.1129 Evaluate side-chains 117 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0736 time to fit residues: 1.3295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 71 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7778 moved from start: 0.7723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6889 Z= 0.205 Angle : 0.745 16.054 9376 Z= 0.355 Chirality : 0.045 0.415 1102 Planarity : 0.004 0.045 1177 Dihedral : 5.537 70.290 915 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.14 % Allowed : 27.41 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.29), residues: 843 helix: 0.66 (0.23), residues: 531 sheet: -2.09 (0.70), residues: 50 loop : -1.01 (0.38), residues: 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.743 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.1515 time to fit residues: 24.4038 Evaluate side-chains 109 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0592 time to fit residues: 1.0990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 0.0470 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.089443 restraints weight = 24659.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093664 restraints weight = 11335.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096125 restraints weight = 7080.224| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.7893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6889 Z= 0.208 Angle : 0.746 14.827 9376 Z= 0.357 Chirality : 0.045 0.412 1102 Planarity : 0.004 0.045 1177 Dihedral : 5.567 71.031 915 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.27 % Allowed : 27.82 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 843 helix: 0.69 (0.23), residues: 531 sheet: -2.07 (0.70), residues: 50 loop : -1.01 (0.38), residues: 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.29 seconds wall clock time: 32 minutes 34.83 seconds (1954.83 seconds total)