Starting phenix.real_space_refine on Mon Sep 23 18:48:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfb_19117/09_2024/8rfb_19117_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfb_19117/09_2024/8rfb_19117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfb_19117/09_2024/8rfb_19117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfb_19117/09_2024/8rfb_19117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfb_19117/09_2024/8rfb_19117_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfb_19117/09_2024/8rfb_19117_neut.cif" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 2979 2.51 5 N 765 2.21 5 O 864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4632 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4632 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 32, 'TRANS': 564} Chain breaks: 2 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 15, 'ASN:plan1': 1, 'ASP:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Time building chain proxies: 3.21, per 1000 atoms: 0.69 Number of scatterers: 4632 At special positions: 0 Unit cell: (69.39, 74.9412, 103.622, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 864 8.00 N 765 7.00 C 2979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 538 " distance=2.67 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False amino acid link not found "ATOM 2671 SD MET A 458 .*. S " "ATOM 3289 SG CYS A 538 .*. S " Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 599.2 milliseconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 9 sheets defined 22.9% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.816A pdb=" N HIS A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 546 removed outlier: 4.175A pdb=" N GLY A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 561 through 572 Processing helix chain 'A' and resid 573 through 576 Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 613 through 624 Processing helix chain 'A' and resid 649 through 672 removed outlier: 3.593A pdb=" N ILE A 653 " --> pdb=" O PRO A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 117 removed outlier: 6.584A pdb=" N LEU A 129 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 163 removed outlier: 6.515A pdb=" N LYS A 173 " --> pdb=" O ASP A 159 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE A 161 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA A 171 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL A 163 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR A 169 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS A 188 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET A 195 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 209 removed outlier: 7.554A pdb=" N VAL A 202 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLN A 222 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 204 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS A 228 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N THR A 246 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 230 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258 removed outlier: 7.476A pdb=" N VAL A 277 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 305 removed outlier: 5.882A pdb=" N ARG A 326 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU A 339 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 354 removed outlier: 6.958A pdb=" N PHE A 362 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 352 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 360 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N MET A 354 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N HIS A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 395 removed outlier: 3.524A pdb=" N CYS A 409 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER A 410 " --> pdb=" O PRO A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 445 removed outlier: 6.257A pdb=" N LEU A 475 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS A 507 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N HIS A 477 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU A 474 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR A 556 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 476 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N PHE A 558 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL A 478 " --> pdb=" O PHE A 558 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR A 553 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N THR A 580 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 555 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLU A 582 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA A 557 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 449 193 hydrogen bonds defined for protein. 528 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: 1.37 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 881 1.32 - 1.45: 1301 1.45 - 1.57: 2530 1.57 - 1.70: 3 1.70 - 1.83: 34 Bond restraints: 4749 Sorted by residual: bond pdb=" CA GLY A 513 " pdb=" C GLY A 513 " ideal model delta sigma weight residual 1.511 1.553 -0.042 1.03e-02 9.43e+03 1.67e+01 bond pdb=" CA ALA A 583 " pdb=" C ALA A 583 " ideal model delta sigma weight residual 1.534 1.496 0.038 9.50e-03 1.11e+04 1.58e+01 bond pdb=" N PRO A 584 " pdb=" CA PRO A 584 " ideal model delta sigma weight residual 1.466 1.418 0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" CB HIS A 638 " pdb=" CG HIS A 638 " ideal model delta sigma weight residual 1.497 1.446 0.051 1.40e-02 5.10e+03 1.34e+01 bond pdb=" C ASN A 271 " pdb=" N LYS A 272 " ideal model delta sigma weight residual 1.333 1.278 0.054 1.50e-02 4.44e+03 1.32e+01 ... (remaining 4744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 5813 2.65 - 5.29: 588 5.29 - 7.94: 62 7.94 - 10.59: 7 10.59 - 13.24: 1 Bond angle restraints: 6471 Sorted by residual: angle pdb=" C ASP A 249 " pdb=" N PRO A 250 " pdb=" CA PRO A 250 " ideal model delta sigma weight residual 119.56 127.86 -8.30 1.02e+00 9.61e-01 6.62e+01 angle pdb=" C THR A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta sigma weight residual 119.56 127.40 -7.84 1.01e+00 9.80e-01 6.02e+01 angle pdb=" C ARG A 413 " pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta sigma weight residual 119.66 125.07 -5.41 7.30e-01 1.88e+00 5.50e+01 angle pdb=" C PRO A 387 " pdb=" N PRO A 388 " pdb=" CA PRO A 388 " ideal model delta sigma weight residual 119.56 126.87 -7.31 1.02e+00 9.61e-01 5.14e+01 angle pdb=" N ASN A 241 " pdb=" CA ASN A 241 " pdb=" C ASN A 241 " ideal model delta sigma weight residual 107.98 121.22 -13.24 1.88e+00 2.83e-01 4.96e+01 ... (remaining 6466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2686 17.98 - 35.96: 101 35.96 - 53.95: 19 53.95 - 71.93: 14 71.93 - 89.91: 2 Dihedral angle restraints: 2822 sinusoidal: 1069 harmonic: 1753 Sorted by residual: dihedral pdb=" CA ARG A 524 " pdb=" C ARG A 524 " pdb=" N LEU A 525 " pdb=" CA LEU A 525 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASP A 713 " pdb=" CB ASP A 713 " pdb=" CG ASP A 713 " pdb=" OD1 ASP A 713 " ideal model delta sinusoidal sigma weight residual -30.00 -87.32 57.32 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB GLU A 276 " pdb=" CG GLU A 276 " pdb=" CD GLU A 276 " pdb=" OE1 GLU A 276 " ideal model delta sinusoidal sigma weight residual 0.00 89.91 -89.91 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 324 0.056 - 0.112: 222 0.112 - 0.168: 126 0.168 - 0.224: 44 0.224 - 0.280: 16 Chirality restraints: 732 Sorted by residual: chirality pdb=" CG LEU A 589 " pdb=" CB LEU A 589 " pdb=" CD1 LEU A 589 " pdb=" CD2 LEU A 589 " both_signs ideal model delta sigma weight residual False -2.59 -2.87 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE A 269 " pdb=" N ILE A 269 " pdb=" C ILE A 269 " pdb=" CB ILE A 269 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA LEU A 515 " pdb=" N LEU A 515 " pdb=" C LEU A 515 " pdb=" CB LEU A 515 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 729 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 519 " -0.048 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP A 519 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 519 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 519 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 519 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 519 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 519 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 519 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 519 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP A 519 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 257 " -0.041 2.00e-02 2.50e+03 2.39e-02 1.15e+01 pdb=" CG TYR A 257 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 257 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 257 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 257 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 257 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 257 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 257 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 421 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C LYS A 421 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS A 421 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE A 422 " -0.019 2.00e-02 2.50e+03 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 240 2.70 - 3.25: 4391 3.25 - 3.80: 7328 3.80 - 4.35: 9774 4.35 - 4.90: 15427 Nonbonded interactions: 37160 Sorted by model distance: nonbonded pdb=" O HIS A 228 " pdb=" OD1 ASP A 229 " model vdw 2.144 3.040 nonbonded pdb=" O GLU A 603 " pdb=" N GLU A 606 " model vdw 2.329 3.120 nonbonded pdb=" OD2 ASP A 396 " pdb=" ND2 ASN A 398 " model vdw 2.381 3.120 nonbonded pdb=" OD1 ASP A 210 " pdb=" OE1 GLU A 211 " model vdw 2.463 3.040 nonbonded pdb=" O LYS A 168 " pdb=" N LEU A 189 " model vdw 2.463 3.120 ... (remaining 37155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.015 0.076 4749 Z= 1.019 Angle : 1.676 13.235 6471 Z= 1.187 Chirality : 0.096 0.280 732 Planarity : 0.010 0.099 830 Dihedral : 11.236 89.908 1687 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.04 % Allowed : 2.45 % Favored : 95.50 % 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: 0.42 (0.32), residues: 591 helix: 0.82 (0.45), residues: 102 sheet: 1.14 (0.36), residues: 181 loop : -0.41 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.007 TRP A 519 HIS 0.008 0.002 HIS A 616 PHE 0.027 0.003 PHE A 218 TYR 0.042 0.006 TYR A 257 ARG 0.006 0.001 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8855 (m100) cc_final: 0.8528 (m100) REVERT: A 278 TRP cc_start: 0.8463 (m100) cc_final: 0.7825 (m100) REVERT: A 291 LEU cc_start: 0.8252 (tp) cc_final: 0.8009 (tt) REVERT: A 347 THR cc_start: 0.8325 (p) cc_final: 0.8070 (p) REVERT: A 357 ASP cc_start: 0.7081 (m-30) cc_final: 0.6704 (m-30) REVERT: A 427 LEU cc_start: 0.7624 (tp) cc_final: 0.7387 (pt) REVERT: A 429 GLU cc_start: 0.7842 (mp0) cc_final: 0.7501 (mp0) REVERT: A 462 HIS cc_start: 0.8286 (p90) cc_final: 0.7905 (p90) REVERT: A 601 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8487 (tt) REVERT: A 621 LYS cc_start: 0.8190 (tttt) cc_final: 0.7846 (tppt) outliers start: 10 outliers final: 1 residues processed: 217 average time/residue: 0.1765 time to fit residues: 47.5297 Evaluate side-chains 116 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 346 ASN A 365 HIS A 470 GLN A 616 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4749 Z= 0.231 Angle : 0.678 6.857 6471 Z= 0.365 Chirality : 0.047 0.169 732 Planarity : 0.004 0.029 830 Dihedral : 5.149 20.692 639 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.20 % Allowed : 4.09 % Favored : 95.71 % 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: 0.46 (0.33), residues: 591 helix: 1.19 (0.46), residues: 113 sheet: 0.76 (0.37), residues: 180 loop : -0.27 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 502 HIS 0.004 0.001 HIS A 228 PHE 0.010 0.002 PHE A 705 TYR 0.029 0.002 TYR A 169 ARG 0.006 0.001 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.8954 (mm) cc_final: 0.8712 (mm) REVERT: A 189 LEU cc_start: 0.8087 (mt) cc_final: 0.7438 (tp) REVERT: A 207 TRP cc_start: 0.8671 (m100) cc_final: 0.8431 (m100) REVERT: A 230 VAL cc_start: 0.9233 (t) cc_final: 0.9005 (p) REVERT: A 278 TRP cc_start: 0.8480 (m100) cc_final: 0.8112 (m100) REVERT: A 346 ASN cc_start: 0.8416 (m-40) cc_final: 0.8191 (m-40) REVERT: A 418 TYR cc_start: 0.6554 (m-80) cc_final: 0.6100 (m-80) REVERT: A 427 LEU cc_start: 0.8062 (tp) cc_final: 0.7760 (pt) REVERT: A 558 PHE cc_start: 0.8385 (t80) cc_final: 0.8109 (t80) REVERT: A 601 LEU cc_start: 0.9092 (pp) cc_final: 0.8793 (tt) REVERT: A 621 LYS cc_start: 0.8240 (tttt) cc_final: 0.7692 (tppt) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1510 time to fit residues: 31.3860 Evaluate side-chains 104 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.0060 chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4749 Z= 0.264 Angle : 0.654 9.456 6471 Z= 0.351 Chirality : 0.047 0.161 732 Planarity : 0.004 0.035 830 Dihedral : 4.870 17.549 639 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: 0.42 (0.33), residues: 591 helix: 1.41 (0.48), residues: 113 sheet: 0.72 (0.39), residues: 163 loop : -0.34 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 519 HIS 0.007 0.001 HIS A 508 PHE 0.013 0.002 PHE A 264 TYR 0.014 0.002 TYR A 623 ARG 0.002 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.9051 (mm) cc_final: 0.8847 (mm) REVERT: A 229 ASP cc_start: 0.8101 (m-30) cc_final: 0.6979 (m-30) REVERT: A 261 ASP cc_start: 0.8644 (p0) cc_final: 0.8298 (p0) REVERT: A 278 TRP cc_start: 0.8534 (m100) cc_final: 0.7960 (m100) REVERT: A 327 THR cc_start: 0.7473 (t) cc_final: 0.7200 (t) REVERT: A 346 ASN cc_start: 0.8262 (m-40) cc_final: 0.7973 (m-40) REVERT: A 354 MET cc_start: 0.8642 (tpp) cc_final: 0.8338 (tpt) REVERT: A 427 LEU cc_start: 0.8163 (tp) cc_final: 0.7911 (pt) REVERT: A 500 ASP cc_start: 0.8479 (t70) cc_final: 0.7981 (t0) REVERT: A 601 LEU cc_start: 0.9179 (pp) cc_final: 0.8847 (tt) REVERT: A 621 LYS cc_start: 0.8352 (tttt) cc_final: 0.7796 (tppt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1533 time to fit residues: 27.9522 Evaluate side-chains 103 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4749 Z= 0.201 Angle : 0.587 7.155 6471 Z= 0.319 Chirality : 0.046 0.161 732 Planarity : 0.004 0.036 830 Dihedral : 4.769 17.610 639 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: 0.54 (0.34), residues: 591 helix: 1.55 (0.48), residues: 113 sheet: 0.91 (0.38), residues: 170 loop : -0.38 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 207 HIS 0.004 0.001 HIS A 477 PHE 0.008 0.001 PHE A 235 TYR 0.031 0.002 TYR A 623 ARG 0.002 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8502 (tmm) cc_final: 0.8217 (tmm) REVERT: A 229 ASP cc_start: 0.7794 (m-30) cc_final: 0.6942 (m-30) REVERT: A 245 TYR cc_start: 0.8220 (t80) cc_final: 0.7886 (t80) REVERT: A 261 ASP cc_start: 0.8670 (p0) cc_final: 0.8363 (p0) REVERT: A 346 ASN cc_start: 0.8099 (m-40) cc_final: 0.7838 (m-40) REVERT: A 367 ASN cc_start: 0.8669 (t0) cc_final: 0.8454 (t0) REVERT: A 427 LEU cc_start: 0.8171 (tp) cc_final: 0.7952 (pt) REVERT: A 500 ASP cc_start: 0.8557 (t70) cc_final: 0.8069 (t0) REVERT: A 601 LEU cc_start: 0.9166 (pp) cc_final: 0.8850 (tt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1345 time to fit residues: 25.1269 Evaluate side-chains 103 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 50.0000 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4749 Z= 0.250 Angle : 0.613 6.695 6471 Z= 0.329 Chirality : 0.045 0.144 732 Planarity : 0.004 0.040 830 Dihedral : 4.785 16.158 639 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: 0.36 (0.34), residues: 591 helix: 1.43 (0.49), residues: 113 sheet: 0.82 (0.39), residues: 170 loop : -0.54 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 207 HIS 0.007 0.001 HIS A 228 PHE 0.025 0.002 PHE A 705 TYR 0.017 0.002 TYR A 301 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.9007 (mm) cc_final: 0.8774 (mm) REVERT: A 207 TRP cc_start: 0.8843 (m100) cc_final: 0.8229 (m100) REVERT: A 245 TYR cc_start: 0.8282 (t80) cc_final: 0.7933 (t80) REVERT: A 261 ASP cc_start: 0.8625 (p0) cc_final: 0.8308 (p0) REVERT: A 346 ASN cc_start: 0.8049 (m-40) cc_final: 0.7780 (m-40) REVERT: A 427 LEU cc_start: 0.8244 (tp) cc_final: 0.7978 (pt) REVERT: A 500 ASP cc_start: 0.8597 (t70) cc_final: 0.8103 (t0) REVERT: A 601 LEU cc_start: 0.9207 (pp) cc_final: 0.8913 (tt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1339 time to fit residues: 21.7643 Evaluate side-chains 89 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.1980 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS A 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4749 Z= 0.190 Angle : 0.578 6.368 6471 Z= 0.312 Chirality : 0.045 0.153 732 Planarity : 0.004 0.039 830 Dihedral : 4.695 16.722 639 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 0.40 (0.34), residues: 591 helix: 1.56 (0.50), residues: 114 sheet: 0.83 (0.39), residues: 170 loop : -0.54 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 519 HIS 0.004 0.001 HIS A 477 PHE 0.008 0.001 PHE A 120 TYR 0.017 0.001 TYR A 623 ARG 0.002 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.8990 (mm) cc_final: 0.8780 (mm) REVERT: A 207 TRP cc_start: 0.8778 (m100) cc_final: 0.8301 (m100) REVERT: A 245 TYR cc_start: 0.8242 (t80) cc_final: 0.7866 (t80) REVERT: A 261 ASP cc_start: 0.8618 (p0) cc_final: 0.8333 (p0) REVERT: A 346 ASN cc_start: 0.7933 (m-40) cc_final: 0.7672 (m-40) REVERT: A 367 ASN cc_start: 0.8686 (t0) cc_final: 0.8445 (t0) REVERT: A 427 LEU cc_start: 0.8240 (tp) cc_final: 0.7964 (pt) REVERT: A 500 ASP cc_start: 0.8625 (t70) cc_final: 0.8134 (t0) REVERT: A 601 LEU cc_start: 0.9229 (pp) cc_final: 0.8962 (tt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1398 time to fit residues: 23.8586 Evaluate side-chains 94 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.0050 chunk 56 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 628 ASN A 644 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4749 Z= 0.182 Angle : 0.576 6.700 6471 Z= 0.309 Chirality : 0.045 0.151 732 Planarity : 0.004 0.037 830 Dihedral : 4.585 15.811 639 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.20 % Allowed : 1.43 % Favored : 98.36 % 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: 0.50 (0.34), residues: 591 helix: 1.77 (0.50), residues: 114 sheet: 0.96 (0.40), residues: 170 loop : -0.58 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 389 HIS 0.004 0.001 HIS A 228 PHE 0.013 0.001 PHE A 362 TYR 0.017 0.001 TYR A 623 ARG 0.003 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8626 (mt-10) REVERT: A 207 TRP cc_start: 0.8780 (m100) cc_final: 0.8199 (m100) REVERT: A 229 ASP cc_start: 0.8063 (m-30) cc_final: 0.7088 (m-30) REVERT: A 245 TYR cc_start: 0.8190 (t80) cc_final: 0.7870 (t80) REVERT: A 261 ASP cc_start: 0.8596 (p0) cc_final: 0.8355 (p0) REVERT: A 346 ASN cc_start: 0.7928 (m-40) cc_final: 0.7678 (m-40) REVERT: A 367 ASN cc_start: 0.8734 (t0) cc_final: 0.8465 (t0) REVERT: A 427 LEU cc_start: 0.8275 (tp) cc_final: 0.8025 (pt) REVERT: A 500 ASP cc_start: 0.8664 (t70) cc_final: 0.8238 (t0) REVERT: A 601 LEU cc_start: 0.9237 (pp) cc_final: 0.8988 (tt) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1337 time to fit residues: 23.7155 Evaluate side-chains 95 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4749 Z= 0.231 Angle : 0.589 6.185 6471 Z= 0.314 Chirality : 0.045 0.153 732 Planarity : 0.004 0.038 830 Dihedral : 4.607 15.744 639 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 0.39 (0.34), residues: 591 helix: 1.92 (0.50), residues: 112 sheet: 0.76 (0.39), residues: 169 loop : -0.65 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 389 HIS 0.004 0.001 HIS A 228 PHE 0.008 0.001 PHE A 120 TYR 0.014 0.001 TYR A 301 ARG 0.005 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8845 (m100) cc_final: 0.8242 (m100) REVERT: A 245 TYR cc_start: 0.8196 (t80) cc_final: 0.7807 (t80) REVERT: A 261 ASP cc_start: 0.8621 (p0) cc_final: 0.8380 (p0) REVERT: A 325 MET cc_start: 0.8686 (mmm) cc_final: 0.8269 (mtt) REVERT: A 346 ASN cc_start: 0.7906 (m-40) cc_final: 0.7653 (m-40) REVERT: A 427 LEU cc_start: 0.8317 (tp) cc_final: 0.8051 (pt) REVERT: A 500 ASP cc_start: 0.8724 (t70) cc_final: 0.8370 (t0) REVERT: A 601 LEU cc_start: 0.9250 (pp) cc_final: 0.9025 (tt) REVERT: A 621 LYS cc_start: 0.8509 (tttt) cc_final: 0.8254 (tppt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1374 time to fit residues: 22.3398 Evaluate side-chains 91 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4749 Z= 0.218 Angle : 0.593 5.734 6471 Z= 0.320 Chirality : 0.046 0.172 732 Planarity : 0.004 0.037 830 Dihedral : 4.590 15.892 639 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: 0.27 (0.34), residues: 591 helix: 1.80 (0.51), residues: 112 sheet: 0.60 (0.39), residues: 171 loop : -0.66 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 389 HIS 0.016 0.001 HIS A 228 PHE 0.011 0.001 PHE A 393 TYR 0.014 0.001 TYR A 301 ARG 0.002 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 TRP cc_start: 0.8840 (m100) cc_final: 0.8457 (m100) REVERT: A 231 TYR cc_start: 0.7817 (m-80) cc_final: 0.7616 (m-10) REVERT: A 245 TYR cc_start: 0.8167 (t80) cc_final: 0.7766 (t80) REVERT: A 261 ASP cc_start: 0.8562 (p0) cc_final: 0.8343 (p0) REVERT: A 325 MET cc_start: 0.8637 (mmm) cc_final: 0.8295 (mtt) REVERT: A 346 ASN cc_start: 0.7866 (m-40) cc_final: 0.7613 (m-40) REVERT: A 427 LEU cc_start: 0.8311 (tp) cc_final: 0.8031 (pt) REVERT: A 500 ASP cc_start: 0.8752 (t70) cc_final: 0.8443 (t0) REVERT: A 601 LEU cc_start: 0.9257 (pp) cc_final: 0.9042 (tt) REVERT: A 621 LYS cc_start: 0.8648 (tttt) cc_final: 0.8215 (tppt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1310 time to fit residues: 21.3125 Evaluate side-chains 89 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4749 Z= 0.247 Angle : 0.598 5.506 6471 Z= 0.321 Chirality : 0.045 0.156 732 Planarity : 0.004 0.037 830 Dihedral : 4.615 16.233 639 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 (0.34), residues: 591 helix: 1.86 (0.51), residues: 112 sheet: 0.47 (0.39), residues: 170 loop : -0.77 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 389 HIS 0.012 0.001 HIS A 228 PHE 0.026 0.002 PHE A 490 TYR 0.020 0.001 TYR A 623 ARG 0.003 0.000 ARG A 491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8607 (tmm) cc_final: 0.8400 (tmm) REVERT: A 207 TRP cc_start: 0.8841 (m100) cc_final: 0.8334 (m100) REVERT: A 231 TYR cc_start: 0.7999 (m-80) cc_final: 0.7786 (m-10) REVERT: A 245 TYR cc_start: 0.8160 (t80) cc_final: 0.7712 (t80) REVERT: A 261 ASP cc_start: 0.8549 (p0) cc_final: 0.8331 (p0) REVERT: A 325 MET cc_start: 0.8611 (mmm) cc_final: 0.8393 (mtt) REVERT: A 346 ASN cc_start: 0.7889 (m-40) cc_final: 0.7657 (m-40) REVERT: A 427 LEU cc_start: 0.8325 (tp) cc_final: 0.8004 (pt) REVERT: A 488 MET cc_start: 0.8830 (mmm) cc_final: 0.8078 (mmm) REVERT: A 500 ASP cc_start: 0.8773 (t70) cc_final: 0.8548 (t0) REVERT: A 601 LEU cc_start: 0.9273 (pp) cc_final: 0.9058 (tt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1201 time to fit residues: 18.6895 Evaluate side-chains 83 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 0.0970 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101665 restraints weight = 9013.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105544 restraints weight = 4989.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108142 restraints weight = 3358.411| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4749 Z= 0.251 Angle : 0.609 5.406 6471 Z= 0.325 Chirality : 0.046 0.186 732 Planarity : 0.004 0.038 830 Dihedral : 4.660 16.729 639 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.08 (0.34), residues: 591 helix: 1.74 (0.50), residues: 114 sheet: 0.47 (0.39), residues: 165 loop : -0.82 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 389 HIS 0.013 0.002 HIS A 228 PHE 0.026 0.002 PHE A 490 TYR 0.014 0.001 TYR A 169 ARG 0.002 0.000 ARG A 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1308.80 seconds wall clock time: 23 minutes 59.37 seconds (1439.37 seconds total)