Starting phenix.real_space_refine on Sat Apr 26 19:46:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jf8_61430/04_2025/9jf8_61430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jf8_61430/04_2025/9jf8_61430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jf8_61430/04_2025/9jf8_61430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jf8_61430/04_2025/9jf8_61430.map" model { file = "/net/cci-nas-00/data/ceres_data/9jf8_61430/04_2025/9jf8_61430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jf8_61430/04_2025/9jf8_61430.cif" } resolution = 3.05 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= -0.002 sd= 0.075 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 24 5.16 5 C 2158 2.51 5 N 537 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3266 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3261 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 9, 'TRANS': 385} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.97, per 1000 atoms: 0.91 Number of scatterers: 3266 At special positions: 0 Unit cell: (56.44, 68.89, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 1 15.00 O 546 8.00 N 537 7.00 C 2158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 592 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 355.9 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 60.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.557A pdb=" N LEU A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 471 through 496 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.601A pdb=" N LEU A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 removed outlier: 3.905A pdb=" N ASN A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.504A pdb=" N ARG A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 removed outlier: 3.513A pdb=" N ARG A 599 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.796A pdb=" N PHE A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 650 removed outlier: 3.559A pdb=" N VAL A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 639 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 678 removed outlier: 3.926A pdb=" N LEU A 660 " --> pdb=" O GLY A 656 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TRP A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 715 removed outlier: 3.894A pdb=" N LEU A 713 " --> pdb=" O MET A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 removed outlier: 3.852A pdb=" N ILE A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 761 removed outlier: 3.940A pdb=" N TYR A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 756 " --> pdb=" O ASN A 752 " (cutoff:3.500A) 142 hydrogen bonds defined for protein. 423 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: 0.69 Time building geometry restraints manager: 0.88 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: 565 1.33 - 1.45: 963 1.45 - 1.57: 1792 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 3359 Sorted by residual: bond pdb=" CA ALA A 764 " pdb=" CB ALA A 764 " ideal model delta sigma weight residual 1.525 1.474 0.050 1.47e-02 4.63e+03 1.18e+01 bond pdb=" C GLY A 765 " pdb=" N LYS A 766 " ideal model delta sigma weight residual 1.332 1.289 0.043 1.41e-02 5.03e+03 9.38e+00 bond pdb=" O3 PO4 A 801 " pdb=" P PO4 A 801 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" CA ALA A 764 " pdb=" C ALA A 764 " ideal model delta sigma weight residual 1.526 1.489 0.036 1.22e-02 6.72e+03 8.87e+00 bond pdb=" O2 PO4 A 801 " pdb=" P PO4 A 801 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.73e+00 ... (remaining 3354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 4479 3.37 - 6.73: 63 6.73 - 10.10: 7 10.10 - 13.46: 4 13.46 - 16.83: 2 Bond angle restraints: 4555 Sorted by residual: angle pdb=" N ARG A 768 " pdb=" CA ARG A 768 " pdb=" C ARG A 768 " ideal model delta sigma weight residual 108.76 91.93 16.83 1.58e+00 4.01e-01 1.13e+02 angle pdb=" O ASN A 762 " pdb=" C ASN A 762 " pdb=" N ASN A 763 " ideal model delta sigma weight residual 123.29 112.73 10.56 1.00e+00 1.00e+00 1.11e+02 angle pdb=" CA PHE A 767 " pdb=" CB PHE A 767 " pdb=" CG PHE A 767 " ideal model delta sigma weight residual 113.80 122.48 -8.68 1.00e+00 1.00e+00 7.53e+01 angle pdb=" N VAL A 770 " pdb=" CA VAL A 770 " pdb=" C VAL A 770 " ideal model delta sigma weight residual 108.84 119.03 -10.19 1.32e+00 5.74e-01 5.96e+01 angle pdb=" C ALA A 769 " pdb=" CA ALA A 769 " pdb=" CB ALA A 769 " ideal model delta sigma weight residual 109.03 120.33 -11.30 1.62e+00 3.81e-01 4.87e+01 ... (remaining 4550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 1698 15.40 - 30.80: 193 30.80 - 46.20: 40 46.20 - 61.61: 6 61.61 - 77.01: 3 Dihedral angle restraints: 1940 sinusoidal: 766 harmonic: 1174 Sorted by residual: dihedral pdb=" C ALA A 769 " pdb=" N ALA A 769 " pdb=" CA ALA A 769 " pdb=" CB ALA A 769 " ideal model delta harmonic sigma weight residual -122.60 -142.09 19.49 0 2.50e+00 1.60e-01 6.08e+01 dihedral pdb=" N ALA A 769 " pdb=" C ALA A 769 " pdb=" CA ALA A 769 " pdb=" CB ALA A 769 " ideal model delta harmonic sigma weight residual 122.90 139.84 -16.94 0 2.50e+00 1.60e-01 4.59e+01 dihedral pdb=" CA ASN A 526 " pdb=" C ASN A 526 " pdb=" N ILE A 527 " pdb=" CA ILE A 527 " ideal model delta harmonic sigma weight residual -180.00 -150.21 -29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 1937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 484 0.145 - 0.289: 8 0.289 - 0.434: 2 0.434 - 0.579: 1 0.579 - 0.724: 1 Chirality restraints: 496 Sorted by residual: chirality pdb=" CA ALA A 769 " pdb=" N ALA A 769 " pdb=" C ALA A 769 " pdb=" CB ALA A 769 " both_signs ideal model delta sigma weight residual False 2.48 1.76 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ARG A 768 " pdb=" N ARG A 768 " pdb=" C ARG A 768 " pdb=" CB ARG A 768 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CA PHE A 767 " pdb=" N PHE A 767 " pdb=" C PHE A 767 " pdb=" CB PHE A 767 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 493 not shown) Planarity restraints: 556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 762 " -0.030 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C ASN A 762 " 0.094 2.00e-02 2.50e+03 pdb=" O ASN A 762 " -0.033 2.00e-02 2.50e+03 pdb=" N ASN A 763 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 467 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C LYS A 467 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS A 467 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 468 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 767 " -0.022 2.00e-02 2.50e+03 1.90e-02 6.30e+00 pdb=" CG PHE A 767 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A 767 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 767 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 767 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 767 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 767 " -0.005 2.00e-02 2.50e+03 ... (remaining 553 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 9 2.39 - 3.02: 1522 3.02 - 3.64: 4857 3.64 - 4.27: 7553 4.27 - 4.90: 12057 Nonbonded interactions: 25998 Sorted by model distance: nonbonded pdb=" O GLU A 759 " pdb=" NH2 ARG A 768 " model vdw 1.759 3.120 nonbonded pdb=" OE1 GLU A 759 " pdb=" NH1 ARG A 768 " model vdw 2.248 3.120 nonbonded pdb=" OE2 GLU A 759 " pdb=" O ALA A 764 " model vdw 2.264 3.040 nonbonded pdb=" O ILE A 543 " pdb=" OG SER A 546 " model vdw 2.300 3.040 nonbonded pdb=" N ARG A 768 " pdb=" O ARG A 768 " model vdw 2.326 2.496 ... (remaining 25993 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: 1.600 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3360 Z= 0.287 Angle : 1.051 16.828 4557 Z= 0.630 Chirality : 0.068 0.724 496 Planarity : 0.006 0.062 556 Dihedral : 13.514 77.008 1187 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.53 % 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: -6.51 (0.24), residues: 393 helix: -4.57 (0.12), residues: 265 sheet: None (None), residues: 0 loop : -3.18 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 675 HIS 0.008 0.001 HIS A 725 PHE 0.044 0.002 PHE A 767 TYR 0.017 0.002 TYR A 671 ARG 0.003 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.31875 ( 142) hydrogen bonds : angle 9.99879 ( 423) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.51993 ( 2) covalent geometry : bond 0.00524 ( 3359) covalent geometry : angle 1.05070 ( 4555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 483 MET cc_start: 0.7445 (tpt) cc_final: 0.6945 (tpt) REVERT: A 535 ARG cc_start: 0.8107 (tpp80) cc_final: 0.6167 (ttp-170) REVERT: A 679 LYS cc_start: 0.8878 (mmtm) cc_final: 0.8525 (mmmt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2190 time to fit residues: 19.7458 Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 468 ASN A 701 GLN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.178701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133683 restraints weight = 3660.301| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.15 r_work: 0.3326 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3360 Z= 0.146 Angle : 0.656 12.671 4557 Z= 0.339 Chirality : 0.042 0.163 496 Planarity : 0.005 0.032 556 Dihedral : 5.776 30.499 447 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.30 % Allowed : 12.64 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.34), residues: 393 helix: -2.13 (0.27), residues: 270 sheet: None (None), residues: 0 loop : -3.32 (0.41), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 PHE 0.009 0.001 PHE A 438 TYR 0.013 0.001 TYR A 458 ARG 0.003 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.05320 ( 142) hydrogen bonds : angle 4.45446 ( 423) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.30102 ( 2) covalent geometry : bond 0.00328 ( 3359) covalent geometry : angle 0.65586 ( 4555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 453 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7448 (ttpt) REVERT: A 676 ASP cc_start: 0.8344 (m-30) cc_final: 0.8026 (m-30) REVERT: A 701 GLN cc_start: 0.7577 (tt0) cc_final: 0.7014 (mm-40) REVERT: A 768 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8454 (ptt-90) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.2093 time to fit residues: 16.2086 Evaluate side-chains 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 768 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 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 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.174247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.128748 restraints weight = 3649.415| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.22 r_work: 0.3216 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3360 Z= 0.164 Angle : 0.633 12.652 4557 Z= 0.327 Chirality : 0.042 0.200 496 Planarity : 0.004 0.027 556 Dihedral : 5.609 29.174 447 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 2.59 % Allowed : 10.92 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.40), residues: 393 helix: -0.95 (0.31), residues: 274 sheet: None (None), residues: 0 loop : -3.03 (0.44), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 PHE 0.009 0.001 PHE A 438 TYR 0.015 0.001 TYR A 649 ARG 0.001 0.000 ARG A 620 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 142) hydrogen bonds : angle 3.98862 ( 423) SS BOND : bond 0.00265 ( 1) SS BOND : angle 0.44063 ( 2) covalent geometry : bond 0.00384 ( 3359) covalent geometry : angle 0.63334 ( 4555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.462 Fit side-chains REVERT: A 561 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8235 (mp-120) REVERT: A 676 ASP cc_start: 0.8288 (m-30) cc_final: 0.7997 (m-30) REVERT: A 701 GLN cc_start: 0.7508 (tt0) cc_final: 0.6956 (mm-40) REVERT: A 768 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8599 (ptt-90) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 0.1904 time to fit residues: 14.2831 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 768 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.0040 chunk 33 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS A 561 GLN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.177072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132418 restraints weight = 3711.389| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.17 r_work: 0.3243 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3360 Z= 0.120 Angle : 0.616 16.034 4557 Z= 0.312 Chirality : 0.042 0.196 496 Planarity : 0.003 0.025 556 Dihedral : 5.390 29.189 447 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.45 % Allowed : 11.49 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.41), residues: 393 helix: -0.33 (0.33), residues: 274 sheet: None (None), residues: 0 loop : -2.82 (0.44), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 PHE 0.011 0.001 PHE A 438 TYR 0.012 0.001 TYR A 458 ARG 0.002 0.000 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 142) hydrogen bonds : angle 3.72155 ( 423) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.20482 ( 2) covalent geometry : bond 0.00271 ( 3359) covalent geometry : angle 0.61579 ( 4555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 676 ASP cc_start: 0.8193 (m-30) cc_final: 0.7890 (m-30) REVERT: A 695 ASN cc_start: 0.8376 (t0) cc_final: 0.7929 (t0) REVERT: A 701 GLN cc_start: 0.7437 (tt0) cc_final: 0.7006 (mm-40) REVERT: A 768 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8688 (ptt-90) outliers start: 12 outliers final: 6 residues processed: 60 average time/residue: 0.1883 time to fit residues: 13.6901 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 768 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 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 420 ASN A 690 ASN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.174875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129805 restraints weight = 3693.283| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.20 r_work: 0.3252 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3360 Z= 0.134 Angle : 0.626 16.067 4557 Z= 0.313 Chirality : 0.042 0.195 496 Planarity : 0.003 0.025 556 Dihedral : 5.326 29.234 447 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.45 % Allowed : 12.93 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.43), residues: 393 helix: -0.10 (0.33), residues: 279 sheet: None (None), residues: 0 loop : -2.77 (0.46), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 675 HIS 0.002 0.001 HIS A 730 PHE 0.011 0.001 PHE A 438 TYR 0.012 0.001 TYR A 649 ARG 0.001 0.000 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 142) hydrogen bonds : angle 3.61762 ( 423) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.23481 ( 2) covalent geometry : bond 0.00314 ( 3359) covalent geometry : angle 0.62655 ( 4555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 561 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8146 (mp-120) REVERT: A 676 ASP cc_start: 0.8114 (m-30) cc_final: 0.7801 (m-30) REVERT: A 695 ASN cc_start: 0.8388 (t0) cc_final: 0.7852 (t0) REVERT: A 701 GLN cc_start: 0.7377 (tt0) cc_final: 0.7089 (mm-40) outliers start: 12 outliers final: 7 residues processed: 56 average time/residue: 0.1908 time to fit residues: 12.6835 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.0270 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 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 = 0.3908 r_free = 0.3908 target = 0.174938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129903 restraints weight = 3776.170| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.22 r_work: 0.3259 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3360 Z= 0.130 Angle : 0.632 17.283 4557 Z= 0.313 Chirality : 0.042 0.192 496 Planarity : 0.003 0.025 556 Dihedral : 5.242 29.463 447 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.59 % Allowed : 13.79 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.43), residues: 393 helix: 0.11 (0.33), residues: 279 sheet: None (None), residues: 0 loop : -2.70 (0.47), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 PHE 0.011 0.001 PHE A 438 TYR 0.011 0.001 TYR A 649 ARG 0.006 0.000 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 142) hydrogen bonds : angle 3.55778 ( 423) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.21203 ( 2) covalent geometry : bond 0.00303 ( 3359) covalent geometry : angle 0.63166 ( 4555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.336 Fit side-chains REVERT: A 561 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.7985 (mp-120) REVERT: A 676 ASP cc_start: 0.8100 (m-30) cc_final: 0.7787 (m-30) REVERT: A 695 ASN cc_start: 0.8423 (t0) cc_final: 0.8151 (t0) REVERT: A 701 GLN cc_start: 0.7350 (tt0) cc_final: 0.7099 (mm-40) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.1832 time to fit residues: 12.5042 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 0.0040 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 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 = 0.3940 r_free = 0.3940 target = 0.177511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133632 restraints weight = 3671.576| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.18 r_work: 0.3251 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3360 Z= 0.121 Angle : 0.624 17.404 4557 Z= 0.310 Chirality : 0.043 0.221 496 Planarity : 0.003 0.025 556 Dihedral : 5.137 29.849 447 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.59 % Allowed : 13.79 % Favored : 83.62 % 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: -0.65 (0.44), residues: 393 helix: 0.36 (0.34), residues: 278 sheet: None (None), residues: 0 loop : -2.32 (0.51), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 751 HIS 0.002 0.001 HIS A 760 PHE 0.011 0.001 PHE A 438 TYR 0.012 0.001 TYR A 414 ARG 0.002 0.000 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 142) hydrogen bonds : angle 3.48696 ( 423) SS BOND : bond 0.00156 ( 1) SS BOND : angle 0.13662 ( 2) covalent geometry : bond 0.00280 ( 3359) covalent geometry : angle 0.62380 ( 4555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.367 Fit side-chains REVERT: A 561 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.7894 (mp-120) REVERT: A 676 ASP cc_start: 0.8057 (m-30) cc_final: 0.7764 (m-30) REVERT: A 695 ASN cc_start: 0.8382 (t0) cc_final: 0.7845 (t0) REVERT: A 701 GLN cc_start: 0.7297 (tt0) cc_final: 0.7094 (mm-40) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.1788 time to fit residues: 11.9130 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.0170 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 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 = 0.3924 r_free = 0.3924 target = 0.176411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132235 restraints weight = 3675.629| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.18 r_work: 0.3259 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3360 Z= 0.110 Angle : 0.626 18.155 4557 Z= 0.307 Chirality : 0.042 0.230 496 Planarity : 0.003 0.025 556 Dihedral : 4.991 29.076 447 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.59 % Allowed : 13.22 % Favored : 84.20 % 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 (0.45), residues: 393 helix: 0.47 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.32 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 PHE 0.011 0.001 PHE A 438 TYR 0.011 0.001 TYR A 414 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 142) hydrogen bonds : angle 3.42108 ( 423) SS BOND : bond 0.00124 ( 1) SS BOND : angle 0.11394 ( 2) covalent geometry : bond 0.00250 ( 3359) covalent geometry : angle 0.62593 ( 4555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.362 Fit side-chains REVERT: A 561 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.7883 (mp-120) REVERT: A 676 ASP cc_start: 0.7992 (m-30) cc_final: 0.7704 (m-30) REVERT: A 695 ASN cc_start: 0.8373 (t0) cc_final: 0.7852 (t0) REVERT: A 701 GLN cc_start: 0.7298 (tt0) cc_final: 0.7059 (mm-40) outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.1748 time to fit residues: 11.5273 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 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 = 0.3943 r_free = 0.3943 target = 0.177746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133499 restraints weight = 3721.885| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.20 r_work: 0.3271 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3360 Z= 0.113 Angle : 0.630 17.982 4557 Z= 0.311 Chirality : 0.042 0.232 496 Planarity : 0.003 0.025 556 Dihedral : 4.931 27.934 447 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.45 % Allowed : 12.93 % Favored : 83.62 % 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: -0.38 (0.45), residues: 393 helix: 0.53 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.20 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 675 HIS 0.003 0.001 HIS A 760 PHE 0.011 0.001 PHE A 438 TYR 0.012 0.001 TYR A 414 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 142) hydrogen bonds : angle 3.38752 ( 423) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.06918 ( 2) covalent geometry : bond 0.00258 ( 3359) covalent geometry : angle 0.63051 ( 4555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.371 Fit side-chains REVERT: A 561 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7896 (mp-120) REVERT: A 676 ASP cc_start: 0.8018 (m-30) cc_final: 0.7737 (m-30) REVERT: A 695 ASN cc_start: 0.8396 (t0) cc_final: 0.7881 (t0) REVERT: A 701 GLN cc_start: 0.7290 (tt0) cc_final: 0.7055 (mm-40) REVERT: A 734 ARG cc_start: 0.6804 (mtt180) cc_final: 0.6523 (mtt90) outliers start: 12 outliers final: 10 residues processed: 54 average time/residue: 0.1901 time to fit residues: 12.3060 Evaluate side-chains 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.178254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134329 restraints weight = 3637.055| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.16 r_work: 0.3230 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3360 Z= 0.125 Angle : 0.638 17.985 4557 Z= 0.315 Chirality : 0.042 0.233 496 Planarity : 0.003 0.025 556 Dihedral : 4.951 27.852 447 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.16 % Allowed : 13.51 % Favored : 83.33 % 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: -0.35 (0.45), residues: 393 helix: 0.53 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.13 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 675 HIS 0.003 0.001 HIS A 760 PHE 0.011 0.001 PHE A 438 TYR 0.009 0.001 TYR A 649 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 142) hydrogen bonds : angle 3.44291 ( 423) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.11080 ( 2) covalent geometry : bond 0.00291 ( 3359) covalent geometry : angle 0.63853 ( 4555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 561 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8025 (mp-120) REVERT: A 676 ASP cc_start: 0.8123 (m-30) cc_final: 0.7857 (m-30) REVERT: A 695 ASN cc_start: 0.8447 (t0) cc_final: 0.7976 (t0) REVERT: A 701 GLN cc_start: 0.7419 (tt0) cc_final: 0.6993 (mm-40) REVERT: A 734 ARG cc_start: 0.6866 (mtt180) cc_final: 0.6595 (mtt90) outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.1875 time to fit residues: 12.6480 Evaluate side-chains 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 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 = 0.3898 r_free = 0.3898 target = 0.173636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128874 restraints weight = 3704.237| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.20 r_work: 0.3247 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3360 Z= 0.174 Angle : 0.674 17.766 4557 Z= 0.333 Chirality : 0.045 0.242 496 Planarity : 0.003 0.026 556 Dihedral : 5.090 28.246 447 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.16 % Allowed : 13.22 % Favored : 83.62 % 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: -0.47 (0.45), residues: 393 helix: 0.41 (0.34), residues: 283 sheet: None (None), residues: 0 loop : -2.11 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 692 HIS 0.005 0.001 HIS A 730 PHE 0.010 0.001 PHE A 438 TYR 0.012 0.001 TYR A 472 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 142) hydrogen bonds : angle 3.54062 ( 423) SS BOND : bond 0.00289 ( 1) SS BOND : angle 0.37813 ( 2) covalent geometry : bond 0.00415 ( 3359) covalent geometry : angle 0.67444 ( 4555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2119.49 seconds wall clock time: 37 minutes 4.04 seconds (2224.04 seconds total)