Starting phenix.real_space_refine on Mon Feb 10 23:29:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jf8_61430/02_2025/9jf8_61430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jf8_61430/02_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_61430/02_2025/9jf8_61430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jf8_61430/02_2025/9jf8_61430.map" model { file = "/net/cci-nas-00/data/ceres_data/9jf8_61430/02_2025/9jf8_61430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jf8_61430/02_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-5592/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: 2.57, per 1000 atoms: 0.79 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: 0.78 Conformation dependent library (CDL) restraints added in 483.8 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: 0.33 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: 0.70 Time building geometry restraints manager: 0.93 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.020 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- 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 : 0.356 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: 0.2267 time to fit residues: 20.4490 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 : 0.351 ------------------------------------------------------------------------------- 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: 0.3324 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.86 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 : 0.339 Fit side-chains revert: symmetry clash REVERT: A 453 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7447 (ttpt) REVERT: A 676 ASP cc_start: 0.8345 (m-30) cc_final: 0.8027 (m-30) REVERT: A 701 GLN cc_start: 0.7577 (tt0) cc_final: 0.7012 (mm-40) REVERT: A 768 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8455 (ptt-90) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.2038 time to fit residues: 15.6609 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 : 0.354 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 12 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 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 = 0.3922 r_free = 0.3922 target = 0.175623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.130066 restraints weight = 3642.433| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.20 r_work: 0.3240 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2444 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= 0.199 Angle : 0.607 12.899 4555 Z= 0.312 Chirality : 0.041 0.201 496 Planarity : 0.004 0.026 556 Dihedral : 5.487 28.816 447 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.59 % Allowed : 11.21 % 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 (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: -2.35 (0.40), residues: 393 helix: -0.89 (0.32), residues: 274 sheet: None (None), residues: 0 loop : -2.96 (0.43), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 PHE 0.010 0.001 PHE A 438 TYR 0.014 0.001 TYR A 458 ARG 0.002 0.000 ARG A 533 *********************** 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 67 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.357 Fit side-chains REVERT: A 561 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8205 (mp-120) REVERT: A 676 ASP cc_start: 0.8228 (m-30) cc_final: 0.7928 (m-30) REVERT: A 701 GLN cc_start: 0.7489 (tt0) cc_final: 0.6902 (mm-40) REVERT: A 768 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8534 (ptt-90) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.1838 time to fit residues: 14.5037 Evaluate side-chains 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 556 PHE Chi-restraints excluded: chain A residue 561 GLN 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: 1.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3902 r_free = 0.3902 target = 0.173567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127808 restraints weight = 3717.032| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.24 r_work: 0.3195 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3359 Z= 0.236 Angle : 0.636 15.642 4555 Z= 0.323 Chirality : 0.043 0.196 496 Planarity : 0.003 0.025 556 Dihedral : 5.449 28.958 447 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.74 % Allowed : 11.49 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.41), residues: 393 helix: -0.40 (0.33), residues: 274 sheet: None (None), residues: 0 loop : -2.83 (0.44), residues: 119 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 0.010 0.001 PHE A 438 TYR 0.013 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 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 676 ASP cc_start: 0.8105 (m-30) cc_final: 0.7806 (m-30) REVERT: A 695 ASN cc_start: 0.8375 (t0) cc_final: 0.7887 (t0) REVERT: A 701 GLN cc_start: 0.7340 (tt0) cc_final: 0.7042 (mm-40) REVERT: A 768 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8674 (ptt-90) outliers start: 13 outliers final: 6 residues processed: 57 average time/residue: 0.1938 time to fit residues: 13.1935 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 : 0.340 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 0.0010 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN 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 = 0.3946 r_free = 0.3946 target = 0.178200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133823 restraints weight = 3680.297| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.19 r_work: 0.3279 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 3359 Z= 0.161 Angle : 0.602 16.250 4555 Z= 0.300 Chirality : 0.041 0.195 496 Planarity : 0.003 0.024 556 Dihedral : 5.200 29.124 447 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.87 % Allowed : 14.37 % Favored : 82.76 % 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: -1.08 (0.44), residues: 393 helix: 0.05 (0.34), residues: 278 sheet: None (None), residues: 0 loop : -2.52 (0.50), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 751 HIS 0.002 0.001 HIS A 760 PHE 0.012 0.001 PHE A 438 TYR 0.012 0.001 TYR A 458 ARG 0.003 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 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.460 Fit side-chains REVERT: A 561 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8224 (mp-120) REVERT: A 676 ASP cc_start: 0.8052 (m-30) cc_final: 0.7740 (m-30) REVERT: A 695 ASN cc_start: 0.8339 (t0) cc_final: 0.7752 (t0) REVERT: A 701 GLN cc_start: 0.7317 (tt0) cc_final: 0.7020 (mm-40) outliers start: 10 outliers final: 5 residues processed: 58 average time/residue: 0.1958 time to fit residues: 13.5072 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 702 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 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 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 = 0.3897 r_free = 0.3897 target = 0.174140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128698 restraints weight = 3768.404| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.21 r_work: 0.3227 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 0.043 3359 Z= 0.208 Angle : 0.635 17.093 4555 Z= 0.314 Chirality : 0.042 0.192 496 Planarity : 0.003 0.025 556 Dihedral : 5.188 29.211 447 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % 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: -0.95 (0.44), residues: 393 helix: 0.19 (0.34), residues: 279 sheet: None (None), residues: 0 loop : -2.60 (0.48), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 751 HIS 0.003 0.001 HIS A 760 PHE 0.010 0.001 PHE A 438 TYR 0.011 0.001 TYR A 649 ARG 0.002 0.000 ARG A 768 *********************** 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 : 0.283 Fit side-chains REVERT: A 561 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8105 (mp-120) REVERT: A 676 ASP cc_start: 0.8058 (m-30) cc_final: 0.7755 (m-30) REVERT: A 695 ASN cc_start: 0.8341 (t0) cc_final: 0.7792 (t0) REVERT: A 701 GLN cc_start: 0.7253 (tt0) cc_final: 0.6944 (mm-40) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.1698 time to fit residues: 11.5128 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 : 0.320 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3963 r_free = 0.3963 target = 0.179444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.135722 restraints weight = 3635.130| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.15 r_work: 0.3250 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3040 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= 0.179 Angle : 0.625 17.688 4555 Z= 0.308 Chirality : 0.042 0.216 496 Planarity : 0.003 0.024 556 Dihedral : 5.112 29.500 447 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.59 % Allowed : 14.08 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.44), residues: 393 helix: 0.35 (0.34), residues: 280 sheet: None (None), residues: 0 loop : -2.50 (0.50), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.001 0.000 ARG A 533 *********************** 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 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.372 Fit side-chains REVERT: A 561 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8030 (mp-120) REVERT: A 676 ASP cc_start: 0.8156 (m-30) cc_final: 0.7867 (m-30) REVERT: A 695 ASN cc_start: 0.8382 (t0) cc_final: 0.7878 (t0) REVERT: A 701 GLN cc_start: 0.7377 (tt0) cc_final: 0.6954 (mm-40) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.1871 time to fit residues: 12.2297 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 : 0.367 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.0570 chunk 8 optimal weight: 0.2980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3938 r_free = 0.3938 target = 0.177635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.133203 restraints weight = 3667.143| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.20 r_work: 0.3257 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 3359 Z= 0.161 Angle : 0.613 17.706 4555 Z= 0.303 Chirality : 0.042 0.224 496 Planarity : 0.003 0.024 556 Dihedral : 5.015 29.536 447 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.59 % Allowed : 14.08 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.45), residues: 393 helix: 0.51 (0.34), residues: 278 sheet: None (None), residues: 0 loop : -2.26 (0.52), 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 0.010 0.001 TYR A 649 ARG 0.001 0.000 ARG A 533 *********************** 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 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.369 Fit side-chains REVERT: A 561 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7945 (mp-120) REVERT: A 676 ASP cc_start: 0.7979 (m-30) cc_final: 0.7702 (m-30) REVERT: A 695 ASN cc_start: 0.8323 (t0) cc_final: 0.7783 (t0) REVERT: A 701 GLN cc_start: 0.7262 (tt0) cc_final: 0.6982 (mm-40) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.1803 time to fit residues: 12.0232 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.0050 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3942 r_free = 0.3942 target = 0.177876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133302 restraints weight = 3718.434| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.22 r_work: 0.3272 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3187 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= 0.169 Angle : 0.623 18.478 4555 Z= 0.305 Chirality : 0.042 0.233 496 Planarity : 0.003 0.023 556 Dihedral : 4.975 29.742 447 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.87 % Allowed : 13.79 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.45), residues: 393 helix: 0.51 (0.34), residues: 281 sheet: None (None), residues: 0 loop : -2.36 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 751 HIS 0.004 0.001 HIS A 440 PHE 0.011 0.001 PHE A 438 TYR 0.009 0.001 TYR A 649 ARG 0.001 0.000 ARG A 533 *********************** 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 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.346 Fit side-chains REVERT: A 561 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7980 (mp-120) REVERT: A 676 ASP cc_start: 0.8013 (m-30) cc_final: 0.7718 (m-30) REVERT: A 695 ASN cc_start: 0.8341 (t0) cc_final: 0.7797 (t0) REVERT: A 701 GLN cc_start: 0.7279 (tt0) cc_final: 0.7059 (mm-40) outliers start: 10 outliers final: 9 residues processed: 56 average time/residue: 0.1767 time to fit residues: 12.0293 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 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: 0.8980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3935 r_free = 0.3935 target = 0.177208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132973 restraints weight = 3639.114| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.18 r_work: 0.3250 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3214 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= 0.182 Angle : 0.641 18.643 4555 Z= 0.314 Chirality : 0.042 0.241 496 Planarity : 0.003 0.023 556 Dihedral : 4.975 29.758 447 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.59 % Allowed : 14.08 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.45), residues: 393 helix: 0.60 (0.34), residues: 278 sheet: None (None), residues: 0 loop : -2.18 (0.52), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 675 HIS 0.005 0.001 HIS A 440 PHE 0.011 0.001 PHE A 438 TYR 0.018 0.001 TYR A 649 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 : 0.397 Fit side-chains REVERT: A 561 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7986 (mp-120) REVERT: A 676 ASP cc_start: 0.8009 (m-30) cc_final: 0.7711 (m-30) REVERT: A 695 ASN cc_start: 0.8340 (t0) cc_final: 0.7807 (t0) REVERT: A 701 GLN cc_start: 0.7285 (tt0) cc_final: 0.7011 (mm-40) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.1779 time to fit residues: 11.9842 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 702 LYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3933 r_free = 0.3933 target = 0.177032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.132758 restraints weight = 3687.834| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.19 r_work: 0.3250 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3254 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= 0.182 Angle : 0.639 18.658 4555 Z= 0.314 Chirality : 0.042 0.243 496 Planarity : 0.003 0.023 556 Dihedral : 4.958 28.350 447 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.87 % Allowed : 14.08 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.45), residues: 393 helix: 0.56 (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 0.005 0.001 HIS A 440 PHE 0.011 0.001 PHE A 438 TYR 0.014 0.001 TYR A 649 ARG 0.003 0.000 ARG A 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2024.93 seconds wall clock time: 36 minutes 36.89 seconds (2196.89 seconds total)