Starting phenix.real_space_refine on Wed Mar 5 18:32:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jf8_61430/03_2025/9jf8_61430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jf8_61430/03_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_61430/03_2025/9jf8_61430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jf8_61430/03_2025/9jf8_61430.map" model { file = "/net/cci-nas-00/data/ceres_data/9jf8_61430/03_2025/9jf8_61430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jf8_61430/03_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-5624/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: 2.68, per 1000 atoms: 0.82 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: 0.74 Conformation dependent library (CDL) restraints added in 364.3 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: 0.28 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: 0.90 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.200 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- 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 3359 Z= 0.359 Angle : 1.051 16.828 4555 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 *********************** 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 : 0.326 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: 0.2255 time to fit residues: 20.3100 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 : 0.333 ------------------------------------------------------------------------------- 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 3359 Z= 0.213 Angle : 0.656 12.671 4555 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 *********************** 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 : 0.365 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: 0.1952 time to fit residues: 15.0274 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 : 0.373 ------------------------------------------------------------------------------- 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 3359 Z= 0.247 Angle : 0.633 12.652 4555 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 *********************** 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 : 0.325 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: 0.1826 time to fit residues: 13.7429 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 : 0.325 ------------------------------------------------------------------------------- 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 3359 Z= 0.178 Angle : 0.616 16.034 4555 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 *********************** 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 : 0.324 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: 0.1827 time to fit residues: 13.1592 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 : 0.360 ------------------------------------------------------------------------------- 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 3359 Z= 0.204 Angle : 0.627 16.067 4555 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 *********************** 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 : 0.322 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: 0.1902 time to fit residues: 12.7048 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 : 0.358 ------------------------------------------------------------------------------- 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: 0.2980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.175292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.130226 restraints weight = 3776.238| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.23 r_work: 0.3244 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3359 Z= 0.189 Angle : 0.628 17.324 4555 Z= 0.312 Chirality : 0.042 0.192 496 Planarity : 0.003 0.025 556 Dihedral : 5.224 29.463 447 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.06 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: -0.97 (0.43), residues: 393 helix: 0.16 (0.34), residues: 278 sheet: None (None), residues: 0 loop : -2.54 (0.49), residues: 115 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 *********************** 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 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.345 Fit side-chains REVERT: A 561 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.7970 (mp-120) REVERT: A 676 ASP cc_start: 0.8098 (m-30) cc_final: 0.7781 (m-30) REVERT: A 695 ASN cc_start: 0.8416 (t0) cc_final: 0.8143 (t0) REVERT: A 701 GLN cc_start: 0.7336 (tt0) cc_final: 0.7077 (mm-40) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.1739 time to fit residues: 12.0362 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 : 0.352 ------------------------------------------------------------------------------- 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: 0.7980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.175356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130707 restraints weight = 3668.888| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.20 r_work: 0.3274 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3359 Z= 0.196 Angle : 0.632 17.227 4555 Z= 0.313 Chirality : 0.043 0.227 496 Planarity : 0.003 0.025 556 Dihedral : 5.153 29.795 447 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % 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 (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: -0.78 (0.44), residues: 393 helix: 0.27 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.48 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.002 0.000 ARG A 455 *********************** 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 : 0.318 Fit side-chains REVERT: A 561 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7925 (mp-120) REVERT: A 676 ASP cc_start: 0.8031 (m-30) cc_final: 0.7735 (m-30) REVERT: A 695 ASN cc_start: 0.8379 (t0) cc_final: 0.7843 (t0) REVERT: A 701 GLN cc_start: 0.7308 (tt0) cc_final: 0.7082 (mm-40) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.1817 time to fit residues: 12.0358 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 : 0.366 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.176011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131845 restraints weight = 3675.467| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.18 r_work: 0.3254 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3359 Z= 0.187 Angle : 0.637 17.937 4555 Z= 0.314 Chirality : 0.043 0.231 496 Planarity : 0.003 0.025 556 Dihedral : 5.062 29.766 447 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.30 % Allowed : 13.51 % 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: -0.59 (0.44), residues: 393 helix: 0.40 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.34 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 *********************** 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 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.345 Fit side-chains REVERT: A 561 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7933 (mp-120) REVERT: A 676 ASP cc_start: 0.8033 (m-30) cc_final: 0.7750 (m-30) REVERT: A 695 ASN cc_start: 0.8407 (t0) cc_final: 0.7896 (t0) REVERT: A 701 GLN cc_start: 0.7326 (tt0) cc_final: 0.7110 (mm-40) outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.1866 time to fit residues: 12.2876 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 : 0.345 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 0.0000 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.175920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134234 restraints weight = 3735.065| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.14 r_work: 0.3216 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3359 Z= 0.197 Angle : 0.639 17.834 4555 Z= 0.317 Chirality : 0.043 0.236 496 Planarity : 0.003 0.026 556 Dihedral : 5.046 28.629 447 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.87 % Allowed : 13.22 % 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 (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: -0.52 (0.44), residues: 393 helix: 0.43 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.27 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.002 0.000 ARG A 455 *********************** 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 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.370 Fit side-chains REVERT: A 561 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.7946 (mp-120) REVERT: A 676 ASP cc_start: 0.8072 (m-30) cc_final: 0.7788 (m-30) REVERT: A 695 ASN cc_start: 0.8413 (t0) cc_final: 0.7898 (t0) REVERT: A 701 GLN cc_start: 0.7354 (tt0) cc_final: 0.7150 (mm-40) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.1997 time to fit residues: 13.3970 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 660 LEU 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 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 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 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 = 0.3937 r_free = 0.3937 target = 0.176745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132886 restraints weight = 3651.376| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.16 r_work: 0.3254 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3359 Z= 0.204 Angle : 0.647 17.869 4555 Z= 0.320 Chirality : 0.043 0.246 496 Planarity : 0.003 0.026 556 Dihedral : 5.049 28.643 447 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.21 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 (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: 0.46 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.22 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 675 HIS 0.003 0.001 HIS A 730 PHE 0.011 0.001 PHE A 438 TYR 0.010 0.001 TYR A 414 ARG 0.003 0.000 ARG A 455 ********************** 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 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.355 Fit side-chains REVERT: A 561 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8031 (mp-120) REVERT: A 676 ASP cc_start: 0.8200 (m-30) cc_final: 0.7928 (m-30) REVERT: A 695 ASN cc_start: 0.8454 (t0) cc_final: 0.7983 (t0) REVERT: A 701 GLN cc_start: 0.7459 (tt0) cc_final: 0.7088 (mm-40) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.1804 time to fit residues: 12.1763 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 : 0.327 ------------------------------------------------------------------------------- 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 660 LEU 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 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 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 = 0.3959 r_free = 0.3959 target = 0.178833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.135050 restraints weight = 3697.275| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.20 r_work: 0.3282 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3359 Z= 0.182 Angle : 0.634 17.964 4555 Z= 0.314 Chirality : 0.042 0.242 496 Planarity : 0.003 0.025 556 Dihedral : 4.980 27.144 447 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.30 % Allowed : 13.79 % 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 (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: -0.33 (0.45), residues: 393 helix: 0.55 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.11 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 675 HIS 0.003 0.001 HIS A 760 PHE 0.011 0.001 PHE A 438 TYR 0.010 0.001 TYR A 414 ARG 0.002 0.000 ARG A 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2025.23 seconds wall clock time: 35 minutes 34.75 seconds (2134.75 seconds total)