Starting phenix.real_space_refine on Wed Sep 17 05:36:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n93_49158/09_2025/9n93_49158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n93_49158/09_2025/9n93_49158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n93_49158/09_2025/9n93_49158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n93_49158/09_2025/9n93_49158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n93_49158/09_2025/9n93_49158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n93_49158/09_2025/9n93_49158.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.023 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 38 5.16 5 C 3493 2.51 5 N 848 2.21 5 O 896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5275 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5275 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 1.47, per 1000 atoms: 0.28 Number of scatterers: 5275 At special positions: 0 Unit cell: (86.87, 81.76, 92.71, 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 38 16.00 O 896 8.00 N 848 7.00 C 3493 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 242.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 70.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.500A pdb=" N ILE A 81 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 132 through 160 removed outlier: 4.194A pdb=" N ALA A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 178 through 186 removed outlier: 6.236A pdb=" N ILE A 183 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 184 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 221 removed outlier: 3.787A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 267 through 294 removed outlier: 3.592A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 343 removed outlier: 4.266A pdb=" N GLN A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.897A pdb=" N ILE A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 418 through 437 removed outlier: 4.004A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 466 through 489 Proline residue: A 480 - end of helix removed outlier: 4.049A pdb=" N THR A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 3.555A pdb=" N PHE A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 521 Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 551 through 574 removed outlier: 3.772A pdb=" N GLY A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.531A pdb=" N VAL A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.686A pdb=" N TRP A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 653 removed outlier: 4.224A pdb=" N PHE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 651 " --> pdb=" O ARG A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.848A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 690 Processing helix chain 'A' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 264 removed outlier: 5.159A pdb=" N VAL A 257 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 353 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP A 259 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 351 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN A 261 " --> pdb=" O MET A 349 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET A 349 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS A 263 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 299 326 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1030 1.33 - 1.45: 1367 1.45 - 1.57: 2973 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 5424 Sorted by residual: bond pdb=" C SER A 476 " pdb=" O SER A 476 " ideal model delta sigma weight residual 1.236 1.319 -0.083 1.16e-02 7.43e+03 5.08e+01 bond pdb=" C TRP A 473 " pdb=" O TRP A 473 " ideal model delta sigma weight residual 1.236 1.296 -0.059 1.15e-02 7.56e+03 2.67e+01 bond pdb=" C LEU A 479 " pdb=" O LEU A 479 " ideal model delta sigma weight residual 1.244 1.284 -0.040 9.40e-03 1.13e+04 1.83e+01 bond pdb=" N ASP A 405 " pdb=" CA ASP A 405 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.22e-02 6.72e+03 1.08e+01 bond pdb=" N ILE A 462 " pdb=" CA ILE A 462 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.18e-02 7.18e+03 8.32e+00 ... (remaining 5419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 7190 1.88 - 3.77: 146 3.77 - 5.65: 30 5.65 - 7.53: 7 7.53 - 9.41: 2 Bond angle restraints: 7375 Sorted by residual: angle pdb=" C SER A 486 " pdb=" N THR A 487 " pdb=" CA THR A 487 " ideal model delta sigma weight residual 122.42 131.83 -9.41 1.77e+00 3.19e-01 2.83e+01 angle pdb=" CA PRO A 480 " pdb=" N PRO A 480 " pdb=" CD PRO A 480 " ideal model delta sigma weight residual 112.00 105.12 6.88 1.40e+00 5.10e-01 2.41e+01 angle pdb=" C ILE A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta sigma weight residual 120.46 113.74 6.72 1.37e+00 5.33e-01 2.40e+01 angle pdb=" N GLU A 545 " pdb=" CA GLU A 545 " pdb=" C GLU A 545 " ideal model delta sigma weight residual 114.56 108.79 5.77 1.27e+00 6.20e-01 2.06e+01 angle pdb=" CA ASP A 405 " pdb=" CB ASP A 405 " pdb=" CG ASP A 405 " ideal model delta sigma weight residual 112.60 117.13 -4.53 1.00e+00 1.00e+00 2.05e+01 ... (remaining 7370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 2877 17.75 - 35.50: 221 35.50 - 53.24: 47 53.24 - 70.99: 10 70.99 - 88.74: 3 Dihedral angle restraints: 3158 sinusoidal: 1240 harmonic: 1918 Sorted by residual: dihedral pdb=" CA LEU A 488 " pdb=" C LEU A 488 " pdb=" N LEU A 489 " pdb=" CA LEU A 489 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA VAL A 653 " pdb=" C VAL A 653 " pdb=" N TYR A 654 " pdb=" CA TYR A 654 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA THR A 487 " pdb=" C THR A 487 " pdb=" N LEU A 488 " pdb=" CA LEU A 488 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 3155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 630 0.045 - 0.091: 169 0.091 - 0.136: 35 0.136 - 0.181: 8 0.181 - 0.226: 1 Chirality restraints: 843 Sorted by residual: chirality pdb=" CA ILE A 482 " pdb=" N ILE A 482 " pdb=" C ILE A 482 " pdb=" CB ILE A 482 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU A 479 " pdb=" CB LEU A 479 " pdb=" CD1 LEU A 479 " pdb=" CD2 LEU A 479 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CB VAL A 483 " pdb=" CA VAL A 483 " pdb=" CG1 VAL A 483 " pdb=" CG2 VAL A 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 840 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 479 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A 480 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 418 " 0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C TRP A 418 " -0.068 2.00e-02 2.50e+03 pdb=" O TRP A 418 " 0.025 2.00e-02 2.50e+03 pdb=" N TRP A 419 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 368 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C ASN A 368 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN A 368 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 369 " 0.015 2.00e-02 2.50e+03 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 876 2.76 - 3.29: 5218 3.29 - 3.83: 8864 3.83 - 4.36: 10363 4.36 - 4.90: 17977 Nonbonded interactions: 43298 Sorted by model distance: nonbonded pdb=" OG1 THR A 438 " pdb=" O THR A 523 " model vdw 2.222 3.040 nonbonded pdb=" ND2 ASN A 368 " pdb=" O VAL A 397 " model vdw 2.268 3.120 nonbonded pdb=" OD1 ASP A 169 " pdb=" NE2 GLN A 187 " model vdw 2.309 3.120 nonbonded pdb=" O ASN A 596 " pdb=" ND2 ASN A 600 " model vdw 2.318 3.120 nonbonded pdb=" O LEU A 433 " pdb=" OG1 THR A 437 " model vdw 2.325 3.040 ... (remaining 43293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.820 Find NCS groups from input model: 0.020 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:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 5424 Z= 0.287 Angle : 0.670 9.414 7375 Z= 0.413 Chirality : 0.043 0.226 843 Planarity : 0.006 0.111 902 Dihedral : 13.479 88.738 1914 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.35 % Allowed : 10.05 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.35), residues: 644 helix: 0.89 (0.26), residues: 435 sheet: -1.81 (1.65), residues: 12 loop : -1.29 (0.50), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.018 0.002 TYR A 484 PHE 0.012 0.001 PHE A 618 TRP 0.012 0.001 TRP A 473 HIS 0.002 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 5424) covalent geometry : angle 0.67037 ( 7375) hydrogen bonds : bond 0.12653 ( 326) hydrogen bonds : angle 5.73822 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.203 Fit side-chains REVERT: A 159 CYS cc_start: 0.8336 (m) cc_final: 0.7626 (t) REVERT: A 212 ARG cc_start: 0.6806 (mpt180) cc_final: 0.6520 (ttp80) REVERT: A 216 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7886 (mt0) REVERT: A 318 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6236 (tm-30) REVERT: A 394 LYS cc_start: 0.8196 (mptt) cc_final: 0.7924 (mmtp) REVERT: A 404 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 587 MET cc_start: 0.7456 (mtt) cc_final: 0.7217 (mtp) REVERT: A 606 GLU cc_start: 0.7485 (pt0) cc_final: 0.7190 (mt-10) outliers start: 2 outliers final: 1 residues processed: 86 average time/residue: 0.5211 time to fit residues: 46.9920 Evaluate side-chains 69 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0370 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117476 restraints weight = 6012.855| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.00 r_work: 0.3284 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5424 Z= 0.121 Angle : 0.519 6.890 7375 Z= 0.273 Chirality : 0.040 0.184 843 Planarity : 0.004 0.039 902 Dihedral : 4.240 20.813 705 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.08 % Allowed : 13.34 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.35), residues: 644 helix: 1.25 (0.25), residues: 436 sheet: -1.98 (1.24), residues: 17 loop : -1.45 (0.50), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 80 TYR 0.016 0.002 TYR A 252 PHE 0.011 0.001 PHE A 618 TRP 0.009 0.001 TRP A 473 HIS 0.002 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5424) covalent geometry : angle 0.51907 ( 7375) hydrogen bonds : bond 0.03850 ( 326) hydrogen bonds : angle 4.53151 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.201 Fit side-chains REVERT: A 159 CYS cc_start: 0.8344 (m) cc_final: 0.7551 (t) REVERT: A 212 ARG cc_start: 0.6803 (mpt180) cc_final: 0.6437 (ttp80) REVERT: A 216 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7745 (mt0) REVERT: A 318 GLU cc_start: 0.6613 (tm-30) cc_final: 0.6391 (tm-30) REVERT: A 394 LYS cc_start: 0.8247 (mptt) cc_final: 0.8000 (mptp) REVERT: A 404 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6909 (mm-30) REVERT: A 587 MET cc_start: 0.7360 (mtt) cc_final: 0.7080 (mtp) REVERT: A 593 ASP cc_start: 0.8113 (m-30) cc_final: 0.7745 (m-30) REVERT: A 606 GLU cc_start: 0.7673 (pt0) cc_final: 0.7275 (mt-10) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.4605 time to fit residues: 41.7279 Evaluate side-chains 80 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 698 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 45 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118511 restraints weight = 5944.051| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.98 r_work: 0.3282 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5424 Z= 0.112 Angle : 0.504 7.461 7375 Z= 0.261 Chirality : 0.040 0.170 843 Planarity : 0.004 0.037 902 Dihedral : 4.092 19.762 702 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.47 % Allowed : 14.56 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.35), residues: 644 helix: 1.45 (0.25), residues: 437 sheet: -1.81 (1.22), residues: 17 loop : -1.45 (0.49), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.023 0.001 TYR A 252 PHE 0.009 0.001 PHE A 142 TRP 0.007 0.001 TRP A 418 HIS 0.002 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5424) covalent geometry : angle 0.50379 ( 7375) hydrogen bonds : bond 0.03649 ( 326) hydrogen bonds : angle 4.36743 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.209 Fit side-chains REVERT: A 53 MET cc_start: 0.7674 (tpp) cc_final: 0.7417 (tpp) REVERT: A 159 CYS cc_start: 0.8297 (m) cc_final: 0.7520 (t) REVERT: A 212 ARG cc_start: 0.6823 (mpt180) cc_final: 0.6494 (ttp80) REVERT: A 318 GLU cc_start: 0.6534 (tm-30) cc_final: 0.6116 (pt0) REVERT: A 394 LYS cc_start: 0.8278 (mptt) cc_final: 0.7999 (mttm) REVERT: A 404 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6977 (mm-30) REVERT: A 463 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6467 (pt) REVERT: A 570 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7596 (mmm) REVERT: A 587 MET cc_start: 0.7331 (mtt) cc_final: 0.7053 (mtt) REVERT: A 593 ASP cc_start: 0.8033 (m-30) cc_final: 0.7632 (m-30) REVERT: A 606 GLU cc_start: 0.7726 (pt0) cc_final: 0.7255 (mt-10) REVERT: A 706 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6712 (tp) outliers start: 20 outliers final: 6 residues processed: 86 average time/residue: 0.4738 time to fit residues: 43.0040 Evaluate side-chains 78 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 706 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 33 optimal weight: 0.0270 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115962 restraints weight = 5981.090| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.89 r_work: 0.3257 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5424 Z= 0.147 Angle : 0.533 7.743 7375 Z= 0.274 Chirality : 0.041 0.166 843 Planarity : 0.004 0.037 902 Dihedral : 4.148 19.867 702 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.29 % Allowed : 15.60 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.35), residues: 644 helix: 1.35 (0.25), residues: 439 sheet: -2.03 (1.18), residues: 17 loop : -1.46 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.022 0.002 TYR A 252 PHE 0.010 0.001 PHE A 47 TRP 0.007 0.001 TRP A 418 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5424) covalent geometry : angle 0.53257 ( 7375) hydrogen bonds : bond 0.03851 ( 326) hydrogen bonds : angle 4.42963 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.212 Fit side-chains REVERT: A 159 CYS cc_start: 0.8324 (m) cc_final: 0.7601 (t) REVERT: A 212 ARG cc_start: 0.6999 (mpt180) cc_final: 0.6646 (ttp80) REVERT: A 280 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: A 318 GLU cc_start: 0.6625 (tm-30) cc_final: 0.6112 (pt0) REVERT: A 394 LYS cc_start: 0.8280 (mptt) cc_final: 0.8033 (mptp) REVERT: A 404 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7251 (mt-10) REVERT: A 463 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6480 (pt) REVERT: A 570 MET cc_start: 0.8176 (mmm) cc_final: 0.7815 (mmm) REVERT: A 587 MET cc_start: 0.7415 (mtt) cc_final: 0.7127 (mtp) REVERT: A 593 ASP cc_start: 0.8135 (m-30) cc_final: 0.7748 (m-30) outliers start: 19 outliers final: 8 residues processed: 81 average time/residue: 0.4659 time to fit residues: 39.7743 Evaluate side-chains 76 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS A 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117009 restraints weight = 6106.686| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.94 r_work: 0.3270 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5424 Z= 0.124 Angle : 0.516 7.796 7375 Z= 0.265 Chirality : 0.040 0.159 843 Planarity : 0.004 0.035 902 Dihedral : 4.067 19.598 702 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.99 % Allowed : 15.94 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.35), residues: 644 helix: 1.39 (0.25), residues: 439 sheet: -1.98 (1.17), residues: 17 loop : -1.45 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 80 TYR 0.022 0.001 TYR A 252 PHE 0.008 0.001 PHE A 618 TRP 0.006 0.001 TRP A 418 HIS 0.002 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5424) covalent geometry : angle 0.51559 ( 7375) hydrogen bonds : bond 0.03696 ( 326) hydrogen bonds : angle 4.36818 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.210 Fit side-chains REVERT: A 159 CYS cc_start: 0.8295 (m) cc_final: 0.7609 (t) REVERT: A 212 ARG cc_start: 0.7018 (mpt180) cc_final: 0.6637 (ttp80) REVERT: A 280 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: A 318 GLU cc_start: 0.6568 (tm-30) cc_final: 0.6084 (pt0) REVERT: A 394 LYS cc_start: 0.8281 (mptt) cc_final: 0.8056 (mptp) REVERT: A 404 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7190 (mt-10) REVERT: A 463 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6442 (pt) REVERT: A 570 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7775 (mmm) REVERT: A 587 MET cc_start: 0.7344 (mtt) cc_final: 0.7047 (mtt) REVERT: A 593 ASP cc_start: 0.8087 (m-30) cc_final: 0.7718 (m-30) outliers start: 23 outliers final: 9 residues processed: 82 average time/residue: 0.4750 time to fit residues: 41.1307 Evaluate side-chains 79 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115523 restraints weight = 6071.545| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.99 r_work: 0.3236 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5424 Z= 0.129 Angle : 0.515 7.325 7375 Z= 0.265 Chirality : 0.040 0.161 843 Planarity : 0.004 0.034 902 Dihedral : 4.063 19.427 702 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.99 % Allowed : 17.16 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.35), residues: 644 helix: 1.37 (0.25), residues: 439 sheet: -1.96 (1.17), residues: 17 loop : -1.45 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.021 0.002 TYR A 252 PHE 0.012 0.001 PHE A 155 TRP 0.006 0.001 TRP A 418 HIS 0.002 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5424) covalent geometry : angle 0.51521 ( 7375) hydrogen bonds : bond 0.03708 ( 326) hydrogen bonds : angle 4.36319 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.209 Fit side-chains REVERT: A 159 CYS cc_start: 0.8295 (m) cc_final: 0.7526 (t) REVERT: A 212 ARG cc_start: 0.6886 (mpt180) cc_final: 0.6468 (ttp80) REVERT: A 280 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: A 318 GLU cc_start: 0.6465 (tm-30) cc_final: 0.5938 (pt0) REVERT: A 347 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 394 LYS cc_start: 0.8257 (mptt) cc_final: 0.8025 (mptp) REVERT: A 404 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7196 (mt-10) REVERT: A 463 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6329 (pt) REVERT: A 570 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7606 (mmm) REVERT: A 587 MET cc_start: 0.7300 (mtt) cc_final: 0.7007 (mtt) outliers start: 23 outliers final: 10 residues processed: 84 average time/residue: 0.3998 time to fit residues: 35.7085 Evaluate side-chains 80 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 0.0050 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 0.0050 chunk 5 optimal weight: 0.0010 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118603 restraints weight = 6049.420| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.01 r_work: 0.3294 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5424 Z= 0.103 Angle : 0.495 6.674 7375 Z= 0.254 Chirality : 0.039 0.153 843 Planarity : 0.004 0.033 902 Dihedral : 3.926 18.464 702 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.47 % Allowed : 18.20 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.35), residues: 644 helix: 1.56 (0.25), residues: 437 sheet: -2.01 (1.18), residues: 17 loop : -1.50 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 330 TYR 0.018 0.001 TYR A 252 PHE 0.009 0.001 PHE A 142 TRP 0.011 0.001 TRP A 418 HIS 0.002 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 5424) covalent geometry : angle 0.49479 ( 7375) hydrogen bonds : bond 0.03437 ( 326) hydrogen bonds : angle 4.21352 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.224 Fit side-chains REVERT: A 127 GLN cc_start: 0.8096 (mt0) cc_final: 0.7745 (mt0) REVERT: A 159 CYS cc_start: 0.8244 (m) cc_final: 0.7457 (t) REVERT: A 212 ARG cc_start: 0.6707 (mpt180) cc_final: 0.6343 (ttp80) REVERT: A 250 ASP cc_start: 0.7657 (t0) cc_final: 0.7453 (t0) REVERT: A 280 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: A 318 GLU cc_start: 0.6332 (tm-30) cc_final: 0.5845 (pt0) REVERT: A 347 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 394 LYS cc_start: 0.8289 (mptt) cc_final: 0.8047 (mptp) REVERT: A 404 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7123 (mt-10) REVERT: A 463 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6353 (pt) REVERT: A 587 MET cc_start: 0.7247 (mtt) cc_final: 0.6921 (mtt) REVERT: A 604 GLN cc_start: 0.8304 (mt0) cc_final: 0.7613 (mp10) REVERT: A 706 LEU cc_start: 0.7360 (tp) cc_final: 0.6587 (tp) outliers start: 20 outliers final: 9 residues processed: 85 average time/residue: 0.4491 time to fit residues: 40.3918 Evaluate side-chains 80 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115280 restraints weight = 5950.851| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.99 r_work: 0.3237 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5424 Z= 0.137 Angle : 0.530 7.817 7375 Z= 0.270 Chirality : 0.041 0.160 843 Planarity : 0.004 0.033 902 Dihedral : 4.027 19.505 702 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.81 % Allowed : 18.54 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.35), residues: 644 helix: 1.48 (0.25), residues: 438 sheet: -1.98 (1.18), residues: 17 loop : -1.47 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 417 TYR 0.021 0.002 TYR A 484 PHE 0.019 0.001 PHE A 155 TRP 0.007 0.001 TRP A 418 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5424) covalent geometry : angle 0.53027 ( 7375) hydrogen bonds : bond 0.03760 ( 326) hydrogen bonds : angle 4.32682 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.250 Fit side-chains REVERT: A 127 GLN cc_start: 0.8101 (mt0) cc_final: 0.7835 (mt0) REVERT: A 159 CYS cc_start: 0.8257 (m) cc_final: 0.7478 (t) REVERT: A 212 ARG cc_start: 0.6850 (mpt180) cc_final: 0.6466 (ttp80) REVERT: A 250 ASP cc_start: 0.7713 (t0) cc_final: 0.7507 (t0) REVERT: A 302 LYS cc_start: 0.6373 (mmtm) cc_final: 0.6147 (mmtm) REVERT: A 318 GLU cc_start: 0.6373 (tm-30) cc_final: 0.5811 (pt0) REVERT: A 347 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7956 (mp) REVERT: A 394 LYS cc_start: 0.8279 (mptt) cc_final: 0.8035 (mptp) REVERT: A 404 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7179 (mt-10) REVERT: A 463 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6308 (pt) REVERT: A 484 TYR cc_start: 0.8247 (t80) cc_final: 0.8036 (t80) REVERT: A 587 MET cc_start: 0.7316 (mtt) cc_final: 0.7004 (mtt) REVERT: A 606 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7508 (mt-10) REVERT: A 706 LEU cc_start: 0.7388 (tp) cc_final: 0.6620 (tt) outliers start: 22 outliers final: 13 residues processed: 86 average time/residue: 0.4132 time to fit residues: 37.7649 Evaluate side-chains 85 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115333 restraints weight = 6051.229| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.01 r_work: 0.3236 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5424 Z= 0.132 Angle : 0.527 7.586 7375 Z= 0.269 Chirality : 0.040 0.161 843 Planarity : 0.004 0.034 902 Dihedral : 4.025 19.333 702 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.12 % Allowed : 19.41 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.35), residues: 644 helix: 1.51 (0.25), residues: 437 sheet: -2.03 (1.20), residues: 17 loop : -1.49 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.018 0.001 TYR A 484 PHE 0.009 0.001 PHE A 142 TRP 0.006 0.001 TRP A 418 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5424) covalent geometry : angle 0.52677 ( 7375) hydrogen bonds : bond 0.03706 ( 326) hydrogen bonds : angle 4.32774 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.135 Fit side-chains REVERT: A 127 GLN cc_start: 0.8097 (mt0) cc_final: 0.7829 (mt0) REVERT: A 159 CYS cc_start: 0.8263 (m) cc_final: 0.7496 (t) REVERT: A 212 ARG cc_start: 0.6854 (mpt180) cc_final: 0.6475 (ttp80) REVERT: A 250 ASP cc_start: 0.7744 (t0) cc_final: 0.7538 (t0) REVERT: A 318 GLU cc_start: 0.6258 (tm-30) cc_final: 0.5677 (pt0) REVERT: A 347 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 394 LYS cc_start: 0.8266 (mptt) cc_final: 0.8016 (mptp) REVERT: A 404 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7153 (mt-10) REVERT: A 484 TYR cc_start: 0.8257 (t80) cc_final: 0.8012 (t80) REVERT: A 587 MET cc_start: 0.7335 (mtt) cc_final: 0.7032 (mtt) REVERT: A 706 LEU cc_start: 0.7360 (tp) cc_final: 0.6583 (tp) outliers start: 18 outliers final: 12 residues processed: 83 average time/residue: 0.4138 time to fit residues: 36.3670 Evaluate side-chains 83 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114780 restraints weight = 6043.612| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.01 r_work: 0.3233 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5424 Z= 0.137 Angle : 0.535 7.775 7375 Z= 0.272 Chirality : 0.041 0.161 843 Planarity : 0.004 0.033 902 Dihedral : 4.046 19.503 702 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.95 % Allowed : 19.76 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.35), residues: 644 helix: 1.42 (0.25), residues: 441 sheet: -2.09 (1.25), residues: 17 loop : -1.50 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 228 TYR 0.018 0.002 TYR A 484 PHE 0.016 0.001 PHE A 155 TRP 0.006 0.001 TRP A 418 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5424) covalent geometry : angle 0.53521 ( 7375) hydrogen bonds : bond 0.03749 ( 326) hydrogen bonds : angle 4.35449 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.222 Fit side-chains REVERT: A 159 CYS cc_start: 0.8263 (m) cc_final: 0.7490 (t) REVERT: A 212 ARG cc_start: 0.6845 (mpt180) cc_final: 0.6470 (ttp80) REVERT: A 250 ASP cc_start: 0.7729 (t0) cc_final: 0.7517 (t0) REVERT: A 318 GLU cc_start: 0.6285 (tm-30) cc_final: 0.5659 (pt0) REVERT: A 347 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 394 LYS cc_start: 0.8221 (mptt) cc_final: 0.7967 (mptp) REVERT: A 404 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7173 (mt-10) REVERT: A 587 MET cc_start: 0.7347 (mtt) cc_final: 0.7038 (mtt) REVERT: A 706 LEU cc_start: 0.7344 (tp) cc_final: 0.6571 (tp) outliers start: 17 outliers final: 14 residues processed: 82 average time/residue: 0.4246 time to fit residues: 36.8303 Evaluate side-chains 85 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114903 restraints weight = 6070.114| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.01 r_work: 0.3232 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5424 Z= 0.134 Angle : 0.544 9.695 7375 Z= 0.275 Chirality : 0.041 0.160 843 Planarity : 0.004 0.033 902 Dihedral : 4.032 19.488 702 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.77 % Allowed : 19.93 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.35), residues: 644 helix: 1.47 (0.25), residues: 440 sheet: -2.33 (1.16), residues: 17 loop : -1.53 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.028 0.002 TYR A 362 PHE 0.010 0.001 PHE A 720 TRP 0.006 0.001 TRP A 418 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5424) covalent geometry : angle 0.54441 ( 7375) hydrogen bonds : bond 0.03700 ( 326) hydrogen bonds : angle 4.33282 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2086.88 seconds wall clock time: 36 minutes 22.06 seconds (2182.06 seconds total)