Starting phenix.real_space_refine on Fri Aug 22 13:24:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jf8_61430/08_2025/9jf8_61430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jf8_61430/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jf8_61430/08_2025/9jf8_61430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jf8_61430/08_2025/9jf8_61430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jf8_61430/08_2025/9jf8_61430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jf8_61430/08_2025/9jf8_61430.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.82, per 1000 atoms: 0.25 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: 0.24 Conformation dependent library (CDL) restraints added in 118.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.06 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: 0.26 Time building geometry restraints manager: 0.34 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: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.040 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.720 ------------------------------------------------------------------------------- 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 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: -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 ARG 0.003 0.000 ARG A 755 TYR 0.017 0.002 TYR A 671 PHE 0.044 0.002 PHE A 767 TRP 0.007 0.001 TRP A 675 HIS 0.008 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 3359) covalent geometry : angle 1.05070 ( 4555) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.51993 ( 2) hydrogen bonds : bond 0.31875 ( 142) hydrogen bonds : angle 9.99879 ( 423) *********************** 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 : 0.085 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: 0.0787 time to fit residues: 7.0769 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 : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.178941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133871 restraints weight = 3694.177| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.16 r_work: 0.3248 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2023 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= 0.144 Angle : 0.651 12.591 4557 Z= 0.337 Chirality : 0.042 0.159 496 Planarity : 0.005 0.031 556 Dihedral : 5.765 30.574 447 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.30 % Allowed : 12.93 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.88 (0.34), residues: 393 helix: -2.11 (0.27), residues: 270 sheet: None (None), residues: 0 loop : -3.31 (0.41), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.013 0.001 TYR A 458 PHE 0.009 0.001 PHE A 438 TRP 0.008 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3359) covalent geometry : angle 0.65108 ( 4555) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.28036 ( 2) hydrogen bonds : bond 0.05233 ( 142) hydrogen bonds : angle 4.44472 ( 423) *********************** 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 68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 453 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7310 (ttpt) REVERT: A 676 ASP cc_start: 0.8256 (m-30) cc_final: 0.7941 (m-30) REVERT: A 701 GLN cc_start: 0.7506 (tt0) cc_final: 0.6884 (mm-40) REVERT: A 768 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8413 (ptt-90) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.0815 time to fit residues: 6.1614 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 : 0.080 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3945 r_free = 0.3945 target = 0.177473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132678 restraints weight = 3678.554| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.14 r_work: 0.3234 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2454 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= 0.129 Angle : 0.607 12.800 4557 Z= 0.311 Chirality : 0.041 0.201 496 Planarity : 0.004 0.025 556 Dihedral : 5.436 29.101 447 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.30 % Allowed : 11.49 % Favored : 86.21 % 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: -2.35 (0.40), residues: 393 helix: -0.89 (0.32), residues: 274 sheet: None (None), residues: 0 loop : -2.96 (0.44), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 452 TYR 0.014 0.001 TYR A 649 PHE 0.010 0.001 PHE A 438 TRP 0.006 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3359) covalent geometry : angle 0.60749 ( 4555) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.29690 ( 2) hydrogen bonds : bond 0.04068 ( 142) hydrogen bonds : angle 3.87891 ( 423) *********************** 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 68 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.088 Fit side-chains REVERT: A 676 ASP cc_start: 0.8214 (m-30) cc_final: 0.7929 (m-30) REVERT: A 701 GLN cc_start: 0.7464 (tt0) cc_final: 0.6880 (mm-40) REVERT: A 768 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8505 (ptt90) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 0.0742 time to fit residues: 5.8477 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN A 468 ASN A 690 ASN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.175318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130048 restraints weight = 3666.074| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.20 r_work: 0.3232 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2651 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= 0.155 Angle : 0.644 15.748 4557 Z= 0.325 Chirality : 0.043 0.196 496 Planarity : 0.003 0.025 556 Dihedral : 5.447 29.126 447 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 4.02 % Allowed : 10.92 % 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 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: -1.80 (0.41), residues: 393 helix: -0.43 (0.32), residues: 277 sheet: None (None), residues: 0 loop : -2.96 (0.45), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 694 TYR 0.012 0.001 TYR A 414 PHE 0.010 0.001 PHE A 438 TRP 0.006 0.001 TRP A 675 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3359) covalent geometry : angle 0.64378 ( 4555) SS BOND : bond 0.00231 ( 1) SS BOND : angle 0.28158 ( 2) hydrogen bonds : bond 0.04130 ( 142) hydrogen bonds : angle 3.74220 ( 423) *********************** 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 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.071 Fit side-chains REVERT: A 593 MET cc_start: 0.6893 (mtm) cc_final: 0.6518 (ttt) REVERT: A 676 ASP cc_start: 0.8145 (m-30) cc_final: 0.7842 (m-30) REVERT: A 695 ASN cc_start: 0.8362 (t0) cc_final: 0.7852 (t0) REVERT: A 701 GLN cc_start: 0.7403 (tt0) cc_final: 0.7121 (mm-40) REVERT: A 768 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8713 (ptt-90) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.0695 time to fit residues: 4.6703 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 : 0.093 ------------------------------------------------------------------------------- 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 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 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 3 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN ** 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 = 0.3923 r_free = 0.3923 target = 0.176112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130964 restraints weight = 3633.149| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.20 r_work: 0.3220 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3360 Z= 0.123 Angle : 0.624 16.692 4557 Z= 0.309 Chirality : 0.042 0.181 496 Planarity : 0.003 0.025 556 Dihedral : 5.281 29.777 447 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.87 % Allowed : 13.51 % 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 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: -1.27 (0.43), residues: 393 helix: -0.05 (0.33), residues: 279 sheet: None (None), residues: 0 loop : -2.74 (0.46), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 533 TYR 0.013 0.001 TYR A 649 PHE 0.011 0.001 PHE A 438 TRP 0.006 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3359) covalent geometry : angle 0.62401 ( 4555) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.16434 ( 2) hydrogen bonds : bond 0.03598 ( 142) hydrogen bonds : angle 3.60291 ( 423) *********************** 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: 10 poor density : 50 time to evaluate : 0.103 Fit side-chains REVERT: A 676 ASP cc_start: 0.8185 (m-30) cc_final: 0.7905 (m-30) REVERT: A 695 ASN cc_start: 0.8405 (t0) cc_final: 0.7926 (t0) REVERT: A 701 GLN cc_start: 0.7454 (tt0) cc_final: 0.6992 (mm-40) REVERT: A 768 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8727 (ptt-90) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 0.0716 time to fit residues: 4.7716 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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 702 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 768 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.174681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128671 restraints weight = 3684.928| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.27 r_work: 0.3253 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3360 Z= 0.117 Angle : 0.608 16.931 4557 Z= 0.303 Chirality : 0.041 0.192 496 Planarity : 0.003 0.024 556 Dihedral : 5.126 29.190 447 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.59 % Allowed : 12.93 % Favored : 84.48 % 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 (0.44), residues: 393 helix: 0.22 (0.34), residues: 280 sheet: None (None), residues: 0 loop : -2.53 (0.48), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 533 TYR 0.012 0.001 TYR A 414 PHE 0.012 0.001 PHE A 438 TRP 0.006 0.001 TRP A 751 HIS 0.002 0.001 HIS A 730 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3359) covalent geometry : angle 0.60796 ( 4555) SS BOND : bond 0.00160 ( 1) SS BOND : angle 0.24533 ( 2) hydrogen bonds : bond 0.03384 ( 142) hydrogen bonds : angle 3.49954 ( 423) *********************** 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 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.140 Fit side-chains REVERT: A 676 ASP cc_start: 0.8090 (m-30) cc_final: 0.7788 (m-30) REVERT: A 695 ASN cc_start: 0.8378 (t0) cc_final: 0.7841 (t0) REVERT: A 701 GLN cc_start: 0.7301 (tt0) cc_final: 0.7020 (mm-40) REVERT: A 768 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8679 (ptt-90) outliers start: 9 outliers final: 6 residues processed: 56 average time/residue: 0.0807 time to fit residues: 5.4024 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.072 ------------------------------------------------------------------------------- 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 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 768 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.179066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135272 restraints weight = 3720.047| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.19 r_work: 0.3302 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3116 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= 0.118 Angle : 0.618 17.373 4557 Z= 0.305 Chirality : 0.041 0.198 496 Planarity : 0.003 0.025 556 Dihedral : 5.051 27.823 447 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.87 % Allowed : 12.93 % 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 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 (0.44), residues: 393 helix: 0.42 (0.34), residues: 278 sheet: None (None), residues: 0 loop : -2.26 (0.51), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 455 TYR 0.013 0.001 TYR A 414 PHE 0.011 0.001 PHE A 438 TRP 0.006 0.001 TRP A 675 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3359) covalent geometry : angle 0.61822 ( 4555) SS BOND : bond 0.00129 ( 1) SS BOND : angle 0.10366 ( 2) hydrogen bonds : bond 0.03372 ( 142) hydrogen bonds : angle 3.45310 ( 423) *********************** 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 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.124 Fit side-chains REVERT: A 676 ASP cc_start: 0.8060 (m-30) cc_final: 0.7785 (m-30) REVERT: A 695 ASN cc_start: 0.8366 (t0) cc_final: 0.7839 (t0) REVERT: A 701 GLN cc_start: 0.7295 (tt0) cc_final: 0.7070 (mm-40) REVERT: A 768 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8727 (ptt-90) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.0890 time to fit residues: 5.9032 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.0050 chunk 14 optimal weight: 2.9990 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN ** 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 = 0.3957 r_free = 0.3957 target = 0.179418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135468 restraints weight = 3741.366| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.20 r_work: 0.3277 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.002 0.045 3360 Z= 0.102 Angle : 0.599 17.451 4557 Z= 0.296 Chirality : 0.041 0.228 496 Planarity : 0.003 0.024 556 Dihedral : 4.895 28.283 447 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % 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 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: -0.22 (0.45), residues: 393 helix: 0.66 (0.34), residues: 278 sheet: None (None), residues: 0 loop : -2.09 (0.52), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 455 TYR 0.010 0.001 TYR A 649 PHE 0.011 0.001 PHE A 438 TRP 0.006 0.001 TRP A 751 HIS 0.002 0.001 HIS A 730 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 3359) covalent geometry : angle 0.59901 ( 4555) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.23593 ( 2) hydrogen bonds : bond 0.02999 ( 142) hydrogen bonds : angle 3.38576 ( 423) *********************** 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 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.119 Fit side-chains REVERT: A 676 ASP cc_start: 0.8000 (m-30) cc_final: 0.7711 (m-30) REVERT: A 695 ASN cc_start: 0.8378 (t0) cc_final: 0.7861 (t0) REVERT: A 701 GLN cc_start: 0.7259 (tt0) cc_final: 0.7003 (mm-40) REVERT: A 734 ARG cc_start: 0.6812 (mtt180) cc_final: 0.6533 (mtt90) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.0874 time to fit residues: 5.7959 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN A 725 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.178114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134084 restraints weight = 3696.209| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.17 r_work: 0.3278 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3289 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= 0.128 Angle : 0.627 17.196 4557 Z= 0.311 Chirality : 0.042 0.241 496 Planarity : 0.003 0.025 556 Dihedral : 4.957 27.157 447 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.59 % Allowed : 13.51 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.25 (0.45), residues: 393 helix: 0.64 (0.34), residues: 278 sheet: None (None), residues: 0 loop : -2.12 (0.52), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 455 TYR 0.015 0.001 TYR A 649 PHE 0.010 0.001 PHE A 438 TRP 0.005 0.001 TRP A 675 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3359) covalent geometry : angle 0.62722 ( 4555) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.06257 ( 2) hydrogen bonds : bond 0.03393 ( 142) hydrogen bonds : angle 3.43278 ( 423) *********************** 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 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.131 Fit side-chains REVERT: A 676 ASP cc_start: 0.8200 (m-30) cc_final: 0.7917 (m-30) REVERT: A 695 ASN cc_start: 0.8425 (t0) cc_final: 0.7925 (t0) REVERT: A 701 GLN cc_start: 0.7426 (tt0) cc_final: 0.7042 (mm-40) REVERT: A 725 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6732 (t70) REVERT: A 734 ARG cc_start: 0.6913 (mtt180) cc_final: 0.6643 (mtt90) outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.0819 time to fit residues: 5.2679 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 : 0.126 ------------------------------------------------------------------------------- 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 690 ASN 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 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.177702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133662 restraints weight = 3661.828| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.17 r_work: 0.3239 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3317 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= 0.126 Angle : 0.643 18.648 4557 Z= 0.315 Chirality : 0.042 0.243 496 Planarity : 0.003 0.024 556 Dihedral : 4.949 26.940 447 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.91 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 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: -0.20 (0.45), residues: 393 helix: 0.66 (0.34), residues: 278 sheet: None (None), residues: 0 loop : -2.05 (0.52), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 455 TYR 0.015 0.001 TYR A 649 PHE 0.010 0.001 PHE A 438 TRP 0.006 0.001 TRP A 675 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3359) covalent geometry : angle 0.64282 ( 4555) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.07797 ( 2) hydrogen bonds : bond 0.03433 ( 142) hydrogen bonds : angle 3.45202 ( 423) ********************** 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 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.122 Fit side-chains REVERT: A 676 ASP cc_start: 0.8060 (m-30) cc_final: 0.7772 (m-30) REVERT: A 695 ASN cc_start: 0.8352 (t0) cc_final: 0.7806 (t0) REVERT: A 701 GLN cc_start: 0.7314 (tt0) cc_final: 0.7066 (mm-40) REVERT: A 734 ARG cc_start: 0.6870 (mtt180) cc_final: 0.6592 (mtt90) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.0763 time to fit residues: 4.8405 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 : 0.118 ------------------------------------------------------------------------------- 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 702 LYS Chi-restraints excluded: chain A residue 703 SER 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 23 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.175377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130832 restraints weight = 3750.268| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.21 r_work: 0.3264 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3360 Z= 0.146 Angle : 0.657 18.224 4557 Z= 0.325 Chirality : 0.044 0.259 496 Planarity : 0.003 0.025 556 Dihedral : 5.070 27.061 447 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % 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 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: -0.37 (0.45), residues: 393 helix: 0.52 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.15 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 455 TYR 0.015 0.001 TYR A 649 PHE 0.010 0.001 PHE A 438 TRP 0.007 0.001 TRP A 692 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3359) covalent geometry : angle 0.65730 ( 4555) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.12472 ( 2) hydrogen bonds : bond 0.03830 ( 142) hydrogen bonds : angle 3.54879 ( 423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 984.88 seconds wall clock time: 17 minutes 28.39 seconds (1048.39 seconds total)