Starting phenix.real_space_refine on Sat Apr 26 22:33:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r4d_18886/04_2025/8r4d_18886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r4d_18886/04_2025/8r4d_18886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r4d_18886/04_2025/8r4d_18886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r4d_18886/04_2025/8r4d_18886.map" model { file = "/net/cci-nas-00/data/ceres_data/8r4d_18886/04_2025/8r4d_18886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r4d_18886/04_2025/8r4d_18886.cif" } resolution = 3.88 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= 0.000 sd= 0.153 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 3 5.49 5 S 15 5.16 5 C 2265 2.51 5 N 608 2.21 5 O 682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3573 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2772 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 12, 'TRANS': 358} Chain breaks: 7 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 769 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.78 Number of scatterers: 3573 At special positions: 0 Unit cell: (61.8381, 74.7809, 97.7905, 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 15 16.00 P 3 15.00 O 682 8.00 N 608 7.00 C 2265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 99 " 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: 0.90 Conformation dependent library (CDL) restraints added in 442.3 milliseconds 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 29.9% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.834A pdb=" N LEU A 506 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.631A pdb=" N ASP A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.626A pdb=" N LEU A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 588 Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.512A pdb=" N LEU A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 647 removed outlier: 3.629A pdb=" N ILE A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 661 removed outlier: 4.040A pdb=" N SER A 661 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 678 Processing helix chain 'A' and resid 697 through 710 removed outlier: 3.550A pdb=" N THR A 702 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 705 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.687A pdb=" N ILE A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 872 through 881 Processing sheet with id=AA1, first strand: chain 'A' and resid 490 through 493 removed outlier: 8.611A pdb=" N VAL A 535 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS A 454 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N MET A 537 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS A 456 " --> pdb=" O MET A 537 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU A 539 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 458 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ILE A 565 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A 536 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL A 567 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 538 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 596 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 830 through 834 removed outlier: 3.622A pdb=" N LYS A 844 " --> pdb=" O ALA A 857 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET A 800 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 23 Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.839A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 54 125 hydrogen bonds defined for protein. 354 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: 0.92 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1169 1.34 - 1.46: 786 1.46 - 1.58: 1662 1.58 - 1.69: 5 1.69 - 1.81: 23 Bond restraints: 3645 Sorted by residual: bond pdb=" N GLU A 769 " pdb=" CA GLU A 769 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.54e+00 bond pdb=" C ALA B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.340 1.373 -0.033 2.76e-02 1.31e+03 1.43e+00 bond pdb=" CB PRO B 41 " pdb=" CG PRO B 41 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.56e-01 bond pdb=" CB GLU A 556 " pdb=" CG GLU A 556 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.95e-01 bond pdb=" CG GLU A 556 " pdb=" CD GLU A 556 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.28e-01 ... (remaining 3640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 4722 1.31 - 2.62: 187 2.62 - 3.93: 43 3.93 - 5.24: 13 5.24 - 6.55: 2 Bond angle restraints: 4967 Sorted by residual: angle pdb=" N THR A 749 " pdb=" CA THR A 749 " pdb=" C THR A 749 " ideal model delta sigma weight residual 108.34 111.98 -3.64 1.31e+00 5.83e-01 7.72e+00 angle pdb=" CA GLN A 818 " pdb=" C GLN A 818 " pdb=" N HIS A 819 " ideal model delta sigma weight residual 118.27 114.10 4.17 1.59e+00 3.96e-01 6.88e+00 angle pdb=" C GLU A 769 " pdb=" CA GLU A 769 " pdb=" CB GLU A 769 " ideal model delta sigma weight residual 110.42 115.51 -5.09 1.99e+00 2.53e-01 6.54e+00 angle pdb=" C LYS A 561 " pdb=" N SER A 562 " pdb=" CA SER A 562 " ideal model delta sigma weight residual 120.68 124.52 -3.84 1.52e+00 4.33e-01 6.38e+00 angle pdb=" C MET A 760 " pdb=" N LYS A 761 " pdb=" CA LYS A 761 " ideal model delta sigma weight residual 120.31 116.63 3.68 1.52e+00 4.33e-01 5.85e+00 ... (remaining 4962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 1988 22.03 - 44.06: 130 44.06 - 66.09: 14 66.09 - 88.12: 4 88.12 - 110.15: 2 Dihedral angle restraints: 2138 sinusoidal: 751 harmonic: 1387 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 141.70 -48.70 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" O3B GSP A1201 " pdb=" O3A GSP A1201 " pdb=" PB GSP A1201 " pdb=" PA GSP A1201 " ideal model delta sinusoidal sigma weight residual 93.55 -156.30 -110.15 1 2.00e+01 2.50e-03 3.23e+01 dihedral pdb=" O3A GSP A1201 " pdb=" O3B GSP A1201 " pdb=" PB GSP A1201 " pdb=" PG GSP A1201 " ideal model delta sinusoidal sigma weight residual 195.33 97.50 97.83 1 2.00e+01 2.50e-03 2.73e+01 ... (remaining 2135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 339 0.033 - 0.066: 160 0.066 - 0.099: 52 0.099 - 0.132: 17 0.132 - 0.165: 2 Chirality restraints: 570 Sorted by residual: chirality pdb=" CA ILE A 821 " pdb=" N ILE A 821 " pdb=" C ILE A 821 " pdb=" CB ILE A 821 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA ILE A 565 " pdb=" N ILE A 565 " pdb=" C ILE A 565 " pdb=" CB ILE A 565 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE A 453 " pdb=" N ILE A 453 " pdb=" C ILE A 453 " pdb=" CB ILE A 453 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 567 not shown) Planarity restraints: 631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 803 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" CG ASP A 803 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 803 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 803 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 810 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 811 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 811 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 811 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 588 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 589 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.019 5.00e-02 4.00e+02 ... (remaining 628 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 968 2.81 - 3.33: 3338 3.33 - 3.86: 5640 3.86 - 4.38: 6492 4.38 - 4.90: 10914 Nonbonded interactions: 27352 Sorted by model distance: nonbonded pdb=" N GLU A 686 " pdb=" OE1 GLU A 686 " model vdw 2.289 3.120 nonbonded pdb=" O SER A 711 " pdb=" OG SER A 712 " model vdw 2.327 3.040 nonbonded pdb=" OD1 ASP A 460 " pdb=" NE1 TRP A 551 " model vdw 2.328 3.120 nonbonded pdb=" OG1 THR A 749 " pdb=" OE1 GLU A 752 " model vdw 2.360 3.040 nonbonded pdb=" O LEU A 639 " pdb=" OG1 THR A 643 " model vdw 2.439 3.040 ... (remaining 27347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 0.200 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: 13.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 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 : 0.003 0.040 3646 Z= 0.127 Angle : 0.648 6.553 4969 Z= 0.348 Chirality : 0.043 0.165 570 Planarity : 0.004 0.035 631 Dihedral : 14.853 110.147 1237 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.57 % Favored : 89.78 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.40 % 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: -2.57 (0.37), residues: 460 helix: -0.90 (0.43), residues: 138 sheet: -0.49 (0.46), residues: 115 loop : -3.05 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 514 HIS 0.004 0.001 HIS A 549 PHE 0.007 0.001 PHE A 588 TYR 0.010 0.001 TYR A 767 ARG 0.007 0.001 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.17030 ( 125) hydrogen bonds : angle 7.26146 ( 354) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.90169 ( 2) covalent geometry : bond 0.00275 ( 3645) covalent geometry : angle 0.64738 ( 4967) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 515 ASP cc_start: 0.6318 (p0) cc_final: 0.6002 (p0) REVERT: A 768 ASP cc_start: 0.5049 (p0) cc_final: 0.4820 (p0) REVERT: B 86 MET cc_start: 0.7287 (mmm) cc_final: 0.6979 (mmm) outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.2034 time to fit residues: 19.8166 Evaluate side-chains 71 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 753 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.195719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169403 restraints weight = 4588.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171732 restraints weight = 3447.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173955 restraints weight = 2808.690| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3646 Z= 0.131 Angle : 0.604 6.643 4969 Z= 0.317 Chirality : 0.043 0.149 570 Planarity : 0.004 0.036 631 Dihedral : 9.482 110.365 518 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.22 % Favored : 89.13 % Rotamer: Outliers : 1.49 % Allowed : 9.82 % Favored : 88.69 % 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: -2.47 (0.37), residues: 460 helix: -0.71 (0.44), residues: 133 sheet: -0.41 (0.48), residues: 111 loop : -3.00 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 53 HIS 0.007 0.001 HIS A 449 PHE 0.011 0.001 PHE A 588 TYR 0.020 0.001 TYR A 767 ARG 0.005 0.001 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 125) hydrogen bonds : angle 5.57243 ( 354) SS BOND : bond 0.00120 ( 1) SS BOND : angle 1.13863 ( 2) covalent geometry : bond 0.00299 ( 3645) covalent geometry : angle 0.60332 ( 4967) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 515 ASP cc_start: 0.6413 (p0) cc_final: 0.6171 (p0) REVERT: A 556 GLU cc_start: 0.5966 (tp30) cc_final: 0.5764 (tp30) REVERT: A 581 GLN cc_start: 0.6672 (pp30) cc_final: 0.6095 (pp30) outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 0.1884 time to fit residues: 17.6000 Evaluate side-chains 74 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** 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 = 0.4125 r_free = 0.4125 target = 0.194871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.168131 restraints weight = 4590.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.170196 restraints weight = 3498.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.172504 restraints weight = 2896.404| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3646 Z= 0.155 Angle : 0.619 6.595 4969 Z= 0.326 Chirality : 0.043 0.153 570 Planarity : 0.004 0.036 631 Dihedral : 9.818 111.662 518 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.22 % Favored : 89.13 % Rotamer: Outliers : 2.08 % Allowed : 14.58 % 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: -2.68 (0.37), residues: 460 helix: -0.94 (0.43), residues: 137 sheet: -0.57 (0.47), residues: 111 loop : -3.09 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.006 0.001 HIS A 523 PHE 0.012 0.002 PHE A 588 TYR 0.010 0.001 TYR A 648 ARG 0.005 0.001 ARG A 754 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 125) hydrogen bonds : angle 5.36452 ( 354) SS BOND : bond 0.00272 ( 1) SS BOND : angle 1.19296 ( 2) covalent geometry : bond 0.00357 ( 3645) covalent geometry : angle 0.61879 ( 4967) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 515 ASP cc_start: 0.6292 (p0) cc_final: 0.6001 (p0) REVERT: A 582 LYS cc_start: 0.7042 (mptt) cc_final: 0.6497 (ttpp) REVERT: A 760 MET cc_start: 0.7052 (mtm) cc_final: 0.6587 (mtp) outliers start: 7 outliers final: 6 residues processed: 80 average time/residue: 0.1960 time to fit residues: 18.6608 Evaluate side-chains 81 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain B residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** 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 = 0.4110 r_free = 0.4110 target = 0.193632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.167558 restraints weight = 4624.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.169943 restraints weight = 3533.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.171453 restraints weight = 2914.722| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3646 Z= 0.177 Angle : 0.635 6.415 4969 Z= 0.336 Chirality : 0.044 0.146 570 Planarity : 0.004 0.038 631 Dihedral : 10.202 115.698 518 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.30 % Favored : 88.04 % Rotamer: Outliers : 3.27 % Allowed : 16.07 % Favored : 80.65 % 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: -2.75 (0.37), residues: 460 helix: -1.08 (0.42), residues: 137 sheet: -0.74 (0.47), residues: 111 loop : -2.98 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 53 HIS 0.008 0.002 HIS A 523 PHE 0.013 0.002 PHE A 588 TYR 0.011 0.002 TYR B 114 ARG 0.005 0.001 ARG A 754 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 125) hydrogen bonds : angle 5.39643 ( 354) SS BOND : bond 0.00326 ( 1) SS BOND : angle 1.16006 ( 2) covalent geometry : bond 0.00409 ( 3645) covalent geometry : angle 0.63424 ( 4967) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 556 GLU cc_start: 0.6430 (tp30) cc_final: 0.6186 (tp30) REVERT: A 760 MET cc_start: 0.7140 (mtm) cc_final: 0.6716 (mtp) REVERT: A 831 MET cc_start: 0.5938 (ptp) cc_final: 0.5547 (ptp) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.1824 time to fit residues: 18.3957 Evaluate side-chains 85 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain B residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** 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 = 0.4117 r_free = 0.4117 target = 0.194151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.167955 restraints weight = 4701.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.170558 restraints weight = 3533.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172301 restraints weight = 2862.430| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3646 Z= 0.157 Angle : 0.616 6.385 4969 Z= 0.326 Chirality : 0.044 0.147 570 Planarity : 0.004 0.039 631 Dihedral : 10.162 116.799 518 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.87 % Favored : 88.48 % Rotamer: Outliers : 3.87 % Allowed : 19.05 % Favored : 77.08 % 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: -2.80 (0.36), residues: 460 helix: -1.07 (0.42), residues: 137 sheet: -0.76 (0.46), residues: 111 loop : -3.07 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.004 0.001 HIS A 526 PHE 0.014 0.002 PHE A 588 TYR 0.010 0.001 TYR A 536 ARG 0.004 0.001 ARG A 651 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 125) hydrogen bonds : angle 5.30428 ( 354) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.94199 ( 2) covalent geometry : bond 0.00363 ( 3645) covalent geometry : angle 0.61598 ( 4967) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 556 GLU cc_start: 0.6389 (tp30) cc_final: 0.6187 (tp30) REVERT: A 568 MET cc_start: 0.7466 (mtm) cc_final: 0.6989 (mtm) REVERT: A 582 LYS cc_start: 0.7100 (mptt) cc_final: 0.6351 (ttpp) REVERT: B 86 MET cc_start: 0.7040 (mmm) cc_final: 0.6543 (mtp) outliers start: 13 outliers final: 9 residues processed: 80 average time/residue: 0.1819 time to fit residues: 17.6541 Evaluate side-chains 83 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain B residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN ** A 581 GLN ** 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 = 0.4125 r_free = 0.4125 target = 0.195181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.168986 restraints weight = 4720.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.171448 restraints weight = 3484.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.173580 restraints weight = 2818.523| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3646 Z= 0.120 Angle : 0.596 7.167 4969 Z= 0.309 Chirality : 0.044 0.146 570 Planarity : 0.004 0.037 631 Dihedral : 9.707 112.383 518 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.22 % Favored : 89.13 % Rotamer: Outliers : 4.46 % Allowed : 19.94 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.61 (0.37), residues: 460 helix: -0.72 (0.43), residues: 135 sheet: -0.76 (0.47), residues: 110 loop : -3.00 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 53 HIS 0.003 0.001 HIS A 526 PHE 0.010 0.001 PHE A 588 TYR 0.007 0.001 TYR A 767 ARG 0.003 0.000 ARG A 651 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 125) hydrogen bonds : angle 5.11981 ( 354) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.61685 ( 2) covalent geometry : bond 0.00281 ( 3645) covalent geometry : angle 0.59619 ( 4967) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 582 LYS cc_start: 0.7160 (mptt) cc_final: 0.6473 (ttpp) REVERT: A 824 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.6014 (mmm-85) REVERT: B 86 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6564 (mtp) outliers start: 15 outliers final: 8 residues processed: 85 average time/residue: 0.1777 time to fit residues: 18.0619 Evaluate side-chains 83 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN ** A 581 GLN ** 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 = 0.4126 r_free = 0.4126 target = 0.195102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.169063 restraints weight = 4639.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171200 restraints weight = 3524.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.173250 restraints weight = 2905.483| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3646 Z= 0.137 Angle : 0.647 14.079 4969 Z= 0.328 Chirality : 0.044 0.167 570 Planarity : 0.004 0.037 631 Dihedral : 9.742 111.685 518 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.65 % Favored : 88.70 % Rotamer: Outliers : 3.87 % Allowed : 21.43 % Favored : 74.70 % 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: -2.60 (0.37), residues: 460 helix: -0.80 (0.42), residues: 135 sheet: -0.69 (0.46), residues: 111 loop : -2.98 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.003 0.001 HIS A 456 PHE 0.011 0.001 PHE A 588 TYR 0.017 0.001 TYR A 767 ARG 0.004 0.001 ARG A 651 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 125) hydrogen bonds : angle 5.20134 ( 354) SS BOND : bond 0.00229 ( 1) SS BOND : angle 0.75214 ( 2) covalent geometry : bond 0.00320 ( 3645) covalent geometry : angle 0.64647 ( 4967) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 824 ARG cc_start: 0.6688 (mmm-85) cc_final: 0.6041 (mmm-85) REVERT: B 86 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6583 (mtp) outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.1898 time to fit residues: 18.9978 Evaluate side-chains 87 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN ** A 581 GLN ** 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 = 0.4167 r_free = 0.4167 target = 0.199179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.173454 restraints weight = 4609.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.175892 restraints weight = 3375.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.178073 restraints weight = 2719.935| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5766 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3646 Z= 0.103 Angle : 0.604 12.148 4969 Z= 0.304 Chirality : 0.043 0.151 570 Planarity : 0.004 0.034 631 Dihedral : 8.981 105.597 518 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.35 % Favored : 90.00 % Rotamer: Outliers : 3.57 % Allowed : 21.73 % Favored : 74.70 % 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: -2.31 (0.37), residues: 460 helix: -0.46 (0.45), residues: 135 sheet: -0.44 (0.47), residues: 111 loop : -2.92 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 827 HIS 0.002 0.001 HIS A 526 PHE 0.006 0.001 PHE A 588 TYR 0.011 0.001 TYR A 767 ARG 0.004 0.001 ARG A 651 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 125) hydrogen bonds : angle 4.94411 ( 354) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.36724 ( 2) covalent geometry : bond 0.00238 ( 3645) covalent geometry : angle 0.60437 ( 4967) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 LYS cc_start: 0.7110 (mptt) cc_final: 0.6465 (ttpp) REVERT: A 824 ARG cc_start: 0.6497 (mmm-85) cc_final: 0.6010 (mmm-85) REVERT: B 86 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6578 (mtp) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.1810 time to fit residues: 18.2032 Evaluate side-chains 86 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 98 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 0.0970 chunk 33 optimal weight: 0.0270 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.196313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.172170 restraints weight = 4570.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.172910 restraints weight = 4014.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.175389 restraints weight = 3282.043| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3646 Z= 0.132 Angle : 0.640 11.928 4969 Z= 0.328 Chirality : 0.044 0.152 570 Planarity : 0.004 0.035 631 Dihedral : 9.190 105.675 518 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.22 % Favored : 89.13 % Rotamer: Outliers : 3.57 % Allowed : 22.32 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.31 (0.37), residues: 460 helix: -0.58 (0.44), residues: 135 sheet: -0.32 (0.47), residues: 103 loop : -2.84 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 53 HIS 0.002 0.001 HIS A 449 PHE 0.009 0.001 PHE A 588 TYR 0.015 0.001 TYR A 767 ARG 0.004 0.001 ARG A 651 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 125) hydrogen bonds : angle 5.08832 ( 354) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.80461 ( 2) covalent geometry : bond 0.00309 ( 3645) covalent geometry : angle 0.63999 ( 4967) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 824 ARG cc_start: 0.6582 (mmm-85) cc_final: 0.6123 (mmm-85) REVERT: B 86 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6607 (mtp) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.1797 time to fit residues: 18.0286 Evaluate side-chains 83 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN ** A 581 GLN ** 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 = 0.4149 r_free = 0.4149 target = 0.197538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171285 restraints weight = 4642.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.173737 restraints weight = 3477.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.175890 restraints weight = 2831.236| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3646 Z= 0.129 Angle : 0.644 11.407 4969 Z= 0.329 Chirality : 0.044 0.141 570 Planarity : 0.004 0.035 631 Dihedral : 9.171 104.461 518 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.78 % Favored : 89.57 % Rotamer: Outliers : 3.57 % Allowed : 22.32 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.30 (0.38), residues: 460 helix: -0.65 (0.44), residues: 135 sheet: -0.32 (0.48), residues: 103 loop : -2.76 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 53 HIS 0.003 0.001 HIS A 526 PHE 0.009 0.001 PHE A 588 TYR 0.015 0.001 TYR A 767 ARG 0.004 0.001 ARG A 651 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 125) hydrogen bonds : angle 5.05670 ( 354) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.75893 ( 2) covalent geometry : bond 0.00303 ( 3645) covalent geometry : angle 0.64412 ( 4967) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 582 LYS cc_start: 0.7160 (mptt) cc_final: 0.6477 (ttpp) REVERT: A 824 ARG cc_start: 0.6609 (mmm-85) cc_final: 0.6126 (mmm-85) REVERT: B 86 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6609 (mtp) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.1788 time to fit residues: 17.7901 Evaluate side-chains 86 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN ** A 581 GLN ** 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 = 0.4148 r_free = 0.4148 target = 0.197475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.171094 restraints weight = 4636.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.173486 restraints weight = 3458.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.175881 restraints weight = 2809.154| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3646 Z= 0.121 Angle : 0.630 11.041 4969 Z= 0.322 Chirality : 0.043 0.147 570 Planarity : 0.004 0.035 631 Dihedral : 8.983 102.607 518 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.22 % Favored : 89.13 % Rotamer: Outliers : 3.87 % Allowed : 22.02 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.23 (0.38), residues: 460 helix: -0.60 (0.44), residues: 135 sheet: -0.31 (0.47), residues: 103 loop : -2.70 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 53 HIS 0.002 0.001 HIS A 526 PHE 0.008 0.001 PHE A 588 TYR 0.018 0.001 TYR A 767 ARG 0.005 0.001 ARG A 651 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 125) hydrogen bonds : angle 5.03060 ( 354) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.69709 ( 2) covalent geometry : bond 0.00284 ( 3645) covalent geometry : angle 0.63033 ( 4967) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1562.59 seconds wall clock time: 27 minutes 43.51 seconds (1663.51 seconds total)