Starting phenix.real_space_refine on Sun Mar 10 21:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/03_2024/7slq_25198_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/03_2024/7slq_25198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/03_2024/7slq_25198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/03_2024/7slq_25198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/03_2024/7slq_25198_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/03_2024/7slq_25198_updated.pdb" } resolution = 3.7 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= 0.005 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 53 5.49 5 S 14 5.16 5 C 3269 2.51 5 N 958 2.21 5 O 1157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 531": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B GLU 562": "OE1" <-> "OE2" Residue "B ARG 565": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5451 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1862 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2473 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "R" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1090 Unusual residues: {'G5J': 1} Classifications: {'RNA': 50, 'undetermined': 1} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 37, None: 1} Not linked: pdbres="G5J R 1 " pdbres=" G R 2 " Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 4.10, per 1000 atoms: 0.75 Number of scatterers: 5451 At special positions: 0 Unit cell: (82.39, 92.02, 103.79, 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 14 16.00 P 53 15.00 O 1157 8.00 N 958 7.00 C 3269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 4 sheets defined 41.3% alpha, 11.8% beta 13 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 458 through 464 removed outlier: 4.008A pdb=" N LYS A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.852A pdb=" N HIS A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.793A pdb=" N SER A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 584 through 606 removed outlier: 7.969A pdb=" N ASP A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N GLU A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 626 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 78 through 81 No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 177 through 185 removed outlier: 3.586A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 412 Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 527 through 545 Processing helix chain 'B' and resid 553 through 570 Processing sheet with id= A, first strand: chain 'A' and resid 660 through 663 removed outlier: 3.511A pdb=" N SER A 660 " --> pdb=" O HIS A 682 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 616 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 581 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG A 469 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ASP A 449 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 471 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 554 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP A 474 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 556 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.673A pdb=" N VAL B 69 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.558A pdb=" N ARG B 377 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 153 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 519 through 523 166 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 2.70 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: 1016 1.33 - 1.45: 1622 1.45 - 1.57: 2902 1.57 - 1.69: 106 1.69 - 1.81: 22 Bond restraints: 5668 Sorted by residual: bond pdb=" C3' G5J R 1 " pdb=" O3' G5J R 1 " ideal model delta sigma weight residual 1.404 1.737 -0.333 2.00e-02 2.50e+03 2.78e+02 bond pdb=" C3' G5J R 1 " pdb=" C4' G5J R 1 " ideal model delta sigma weight residual 1.526 1.248 0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C1' G5J R 1 " pdb=" C2' G5J R 1 " ideal model delta sigma weight residual 1.524 1.254 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C6 G5J R 1 " pdb=" O6 G5J R 1 " ideal model delta sigma weight residual 1.226 1.433 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C2' G5J R 1 " pdb=" C3' G5J R 1 " ideal model delta sigma weight residual 1.531 1.722 -0.191 2.00e-02 2.50e+03 9.15e+01 ... (remaining 5663 not shown) Histogram of bond angle deviations from ideal: 91.52 - 101.07: 19 101.07 - 110.62: 2058 110.62 - 120.17: 3512 120.17 - 129.72: 2277 129.72 - 139.28: 58 Bond angle restraints: 7924 Sorted by residual: angle pdb=" C VAL B 99 " pdb=" N VAL B 100 " pdb=" CA VAL B 100 " ideal model delta sigma weight residual 121.97 128.13 -6.16 1.00e+00 1.00e+00 3.80e+01 angle pdb=" O3' A R 298 " pdb=" C3' A R 298 " pdb=" C2' A R 298 " ideal model delta sigma weight residual 109.50 118.39 -8.89 1.50e+00 4.44e-01 3.51e+01 angle pdb=" N TYR B 68 " pdb=" CA TYR B 68 " pdb=" CB TYR B 68 " ideal model delta sigma weight residual 111.05 102.42 8.63 1.50e+00 4.44e-01 3.31e+01 angle pdb=" O3A G5J R 1 " pdb=" PB G5J R 1 " pdb=" O3B G5J R 1 " ideal model delta sigma weight residual 92.82 109.77 -16.95 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C4' G R 300 " pdb=" C3' G R 300 " pdb=" O3' G R 300 " ideal model delta sigma weight residual 109.40 117.58 -8.18 1.50e+00 4.44e-01 2.98e+01 ... (remaining 7919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 3273 35.50 - 71.00: 184 71.00 - 106.51: 23 106.51 - 142.01: 1 142.01 - 177.51: 3 Dihedral angle restraints: 3484 sinusoidal: 1855 harmonic: 1629 Sorted by residual: dihedral pdb=" C5' A R 298 " pdb=" C4' A R 298 " pdb=" C3' A R 298 " pdb=" O3' A R 298 " ideal model delta sinusoidal sigma weight residual 147.00 105.99 41.01 1 8.00e+00 1.56e-02 3.68e+01 dihedral pdb=" CA ASN B 135 " pdb=" C ASN B 135 " pdb=" N VAL B 136 " pdb=" CA VAL B 136 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" C3' G5J R 1 " pdb=" C4' G5J R 1 " pdb=" C5' G5J R 1 " pdb=" O5' G5J R 1 " ideal model delta sinusoidal sigma weight residual 176.65 -0.86 177.51 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 875 0.118 - 0.237: 54 0.237 - 0.355: 2 0.355 - 0.473: 2 0.473 - 0.591: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" C3' A R 298 " pdb=" C4' A R 298 " pdb=" O3' A R 298 " pdb=" C2' A R 298 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CA PRO A 427 " pdb=" N PRO A 427 " pdb=" C PRO A 427 " pdb=" CB PRO A 427 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C3' G5J R 1 " pdb=" C2' G5J R 1 " pdb=" C4' G5J R 1 " pdb=" O3' G5J R 1 " both_signs ideal model delta sigma weight residual False -2.71 -3.10 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 931 not shown) Planarity restraints: 815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 549 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO A 550 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 550 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 550 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G5J R 1 " -0.031 2.00e-02 2.50e+03 1.47e-02 6.50e+00 pdb=" C2 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G5J R 1 " -0.000 2.00e-02 2.50e+03 pdb=" C8 G5J R 1 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G5J R 1 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G5J R 1 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G5J R 1 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G5J R 1 " 0.026 2.00e-02 2.50e+03 pdb=" N9 G5J R 1 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G5J R 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 132 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO B 133 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.032 5.00e-02 4.00e+02 ... (remaining 812 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 185 2.69 - 3.25: 4874 3.25 - 3.80: 8785 3.80 - 4.35: 10870 4.35 - 4.90: 17241 Nonbonded interactions: 41955 Sorted by model distance: nonbonded pdb=" O2' A R 297 " pdb=" OP1 A R 298 " model vdw 2.144 2.440 nonbonded pdb=" O GLY A 532 " pdb=" OH TYR B 391 " model vdw 2.239 2.440 nonbonded pdb=" O SER B 461 " pdb=" OG1 THR B 491 " model vdw 2.331 2.440 nonbonded pdb=" O TYR A 650 " pdb=" OG SER A 653 " model vdw 2.337 2.440 nonbonded pdb=" OD1 ASP A 474 " pdb=" O2' SAH A 701 " model vdw 2.341 2.440 ... (remaining 41950 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 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: 0.010 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.040 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.300 Find NCS groups from input model: 0.140 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 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 : 0.011 0.333 5668 Z= 0.790 Angle : 1.161 16.945 7924 Z= 0.628 Chirality : 0.062 0.591 934 Planarity : 0.007 0.069 815 Dihedral : 19.871 177.509 2430 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.35 % Allowed : 4.94 % Favored : 93.71 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.00 % 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: -2.83 (0.30), residues: 546 helix: -2.16 (0.25), residues: 252 sheet: -0.52 (0.63), residues: 64 loop : -1.76 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 620 HIS 0.005 0.002 HIS B 158 PHE 0.022 0.003 PHE B 168 TYR 0.022 0.003 TYR B 68 ARG 0.009 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 ARG cc_start: 0.7168 (ttm110) cc_final: 0.6914 (ttp-110) outliers start: 6 outliers final: 2 residues processed: 109 average time/residue: 0.2372 time to fit residues: 31.3963 Evaluate side-chains 56 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain B residue 557 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0570 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.0770 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 ASN B 528 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5668 Z= 0.151 Angle : 0.570 8.024 7924 Z= 0.290 Chirality : 0.039 0.228 934 Planarity : 0.005 0.080 815 Dihedral : 21.431 173.641 1442 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.25 % Allowed : 11.46 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.38 (0.32), residues: 546 helix: -0.59 (0.30), residues: 257 sheet: -0.02 (0.74), residues: 47 loop : -1.36 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 140 HIS 0.004 0.001 HIS B 528 PHE 0.024 0.001 PHE B 46 TYR 0.008 0.001 TYR B 483 ARG 0.005 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7470 (t0) cc_final: 0.7250 (t0) REVERT: A 625 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7688 (ptmm) REVERT: A 636 ASN cc_start: 0.8758 (m-40) cc_final: 0.8540 (m-40) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.2157 time to fit residues: 19.0426 Evaluate side-chains 52 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 159 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 ASN B 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5668 Z= 0.194 Angle : 0.562 8.474 7924 Z= 0.288 Chirality : 0.039 0.183 934 Planarity : 0.005 0.082 815 Dihedral : 20.713 174.107 1436 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.72 % Allowed : 10.56 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.67 (0.34), residues: 546 helix: 0.27 (0.32), residues: 249 sheet: 0.17 (0.78), residues: 47 loop : -1.27 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 465 HIS 0.003 0.001 HIS B 52 PHE 0.028 0.001 PHE B 56 TYR 0.012 0.001 TYR A 560 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 51 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7602 (t0) cc_final: 0.7323 (t0) REVERT: B 40 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7361 (ptpp) outliers start: 21 outliers final: 11 residues processed: 66 average time/residue: 0.1626 time to fit residues: 14.4601 Evaluate side-chains 56 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 569 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5668 Z= 0.179 Angle : 0.538 8.167 7924 Z= 0.275 Chirality : 0.038 0.177 934 Planarity : 0.005 0.080 815 Dihedral : 20.450 174.765 1436 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.60 % Allowed : 14.83 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.32 (0.35), residues: 546 helix: 0.60 (0.33), residues: 248 sheet: 0.32 (0.80), residues: 47 loop : -1.11 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 533 HIS 0.003 0.001 HIS B 52 PHE 0.020 0.001 PHE B 56 TYR 0.009 0.001 TYR B 391 ARG 0.005 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7655 (t0) cc_final: 0.7346 (t0) REVERT: B 545 ASN cc_start: 0.7636 (m110) cc_final: 0.6961 (t0) outliers start: 16 outliers final: 10 residues processed: 57 average time/residue: 0.1592 time to fit residues: 12.3774 Evaluate side-chains 50 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 40.0000 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 HIS B 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5668 Z= 0.383 Angle : 0.700 10.725 7924 Z= 0.355 Chirality : 0.044 0.209 934 Planarity : 0.006 0.083 815 Dihedral : 20.504 174.792 1436 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.82 % Allowed : 17.08 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.63 (0.34), residues: 546 helix: 0.36 (0.32), residues: 249 sheet: 0.44 (0.73), residues: 54 loop : -1.43 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 465 HIS 0.006 0.002 HIS A 682 PHE 0.014 0.002 PHE B 56 TYR 0.014 0.002 TYR A 623 ARG 0.005 0.001 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.566 Fit side-chains REVERT: A 461 ILE cc_start: 0.8809 (mm) cc_final: 0.8551 (mm) REVERT: A 576 ASP cc_start: 0.7722 (t0) cc_final: 0.7421 (t0) REVERT: B 79 LYS cc_start: 0.7086 (mtpt) cc_final: 0.6871 (mtpp) REVERT: B 137 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.6634 (t0) outliers start: 17 outliers final: 12 residues processed: 60 average time/residue: 0.1486 time to fit residues: 12.3649 Evaluate side-chains 53 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 569 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 41 GLN B 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5668 Z= 0.154 Angle : 0.547 8.178 7924 Z= 0.273 Chirality : 0.038 0.176 934 Planarity : 0.005 0.083 815 Dihedral : 20.344 176.519 1436 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.04 % Allowed : 18.20 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.26 (0.35), residues: 546 helix: 0.75 (0.33), residues: 250 sheet: 0.18 (0.79), residues: 49 loop : -1.20 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 45 HIS 0.002 0.000 HIS B 52 PHE 0.017 0.001 PHE B 56 TYR 0.014 0.001 TYR B 391 ARG 0.003 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7635 (t0) cc_final: 0.7338 (t0) REVERT: B 40 LYS cc_start: 0.7364 (ptpp) cc_final: 0.7150 (ptpp) REVERT: B 545 ASN cc_start: 0.7753 (p0) cc_final: 0.6974 (p0) outliers start: 18 outliers final: 12 residues processed: 62 average time/residue: 0.1641 time to fit residues: 13.8979 Evaluate side-chains 55 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5668 Z= 0.160 Angle : 0.543 7.626 7924 Z= 0.274 Chirality : 0.038 0.173 934 Planarity : 0.005 0.088 815 Dihedral : 20.228 175.945 1436 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.04 % Allowed : 19.33 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.23 (0.35), residues: 546 helix: 0.73 (0.33), residues: 249 sheet: 0.28 (0.72), residues: 56 loop : -1.18 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 45 HIS 0.002 0.001 HIS B 52 PHE 0.015 0.001 PHE B 56 TYR 0.025 0.001 TYR B 532 ARG 0.006 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7612 (t0) cc_final: 0.7307 (t0) REVERT: A 625 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7844 (ptmm) REVERT: B 40 LYS cc_start: 0.7400 (ptpp) cc_final: 0.7150 (ptpp) REVERT: B 545 ASN cc_start: 0.7785 (p0) cc_final: 0.7110 (p0) outliers start: 18 outliers final: 14 residues processed: 62 average time/residue: 0.1466 time to fit residues: 12.8909 Evaluate side-chains 55 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5668 Z= 0.329 Angle : 0.667 9.384 7924 Z= 0.336 Chirality : 0.042 0.196 934 Planarity : 0.006 0.090 815 Dihedral : 20.208 175.139 1436 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.49 % Allowed : 19.33 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.35), residues: 546 helix: 0.43 (0.33), residues: 249 sheet: 0.13 (0.68), residues: 61 loop : -1.39 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP B 45 HIS 0.004 0.001 HIS B 52 PHE 0.014 0.002 PHE B 56 TYR 0.011 0.002 TYR A 490 ARG 0.005 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8759 (mm) cc_final: 0.8525 (mm) REVERT: A 576 ASP cc_start: 0.7643 (t0) cc_final: 0.7387 (t0) REVERT: B 137 ASN cc_start: 0.6957 (OUTLIER) cc_final: 0.6621 (t0) REVERT: B 545 ASN cc_start: 0.7823 (p0) cc_final: 0.7068 (p0) outliers start: 20 outliers final: 15 residues processed: 62 average time/residue: 0.1541 time to fit residues: 13.4521 Evaluate side-chains 55 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 39 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5668 Z= 0.341 Angle : 0.680 9.881 7924 Z= 0.342 Chirality : 0.042 0.206 934 Planarity : 0.006 0.092 815 Dihedral : 20.186 175.602 1436 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.94 % Allowed : 19.55 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.79 (0.34), residues: 546 helix: 0.21 (0.32), residues: 248 sheet: -0.16 (0.69), residues: 61 loop : -1.36 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.005 TRP A 465 HIS 0.005 0.002 HIS B 52 PHE 0.015 0.002 PHE B 56 TYR 0.011 0.002 TYR B 532 ARG 0.004 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 41 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8726 (mm) cc_final: 0.8510 (mm) REVERT: A 576 ASP cc_start: 0.7647 (t0) cc_final: 0.7372 (t0) REVERT: B 137 ASN cc_start: 0.6939 (OUTLIER) cc_final: 0.6607 (t0) outliers start: 22 outliers final: 19 residues processed: 61 average time/residue: 0.1669 time to fit residues: 14.3747 Evaluate side-chains 58 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 38 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 569 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 0.0470 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 GLN B 33 GLN B 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5668 Z= 0.144 Angle : 0.554 6.825 7924 Z= 0.281 Chirality : 0.037 0.172 934 Planarity : 0.005 0.089 815 Dihedral : 20.058 176.322 1436 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.82 % Allowed : 20.45 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.43 (0.35), residues: 546 helix: 0.59 (0.34), residues: 247 sheet: 0.22 (0.72), residues: 54 loop : -1.30 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 45 HIS 0.003 0.001 HIS B 138 PHE 0.017 0.001 PHE B 56 TYR 0.017 0.001 TYR B 391 ARG 0.004 0.000 ARG B 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.587 Fit side-chains REVERT: A 576 ASP cc_start: 0.7528 (t0) cc_final: 0.7207 (t0) REVERT: B 533 TRP cc_start: 0.4703 (m100) cc_final: 0.4223 (m100) outliers start: 17 outliers final: 15 residues processed: 64 average time/residue: 0.1754 time to fit residues: 15.3593 Evaluate side-chains 59 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.172834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.136816 restraints weight = 9657.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.135723 restraints weight = 10367.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138139 restraints weight = 9355.075| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5668 Z= 0.172 Angle : 0.568 6.972 7924 Z= 0.289 Chirality : 0.038 0.178 934 Planarity : 0.005 0.094 815 Dihedral : 19.991 174.916 1436 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.37 % Allowed : 20.67 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.43 (0.35), residues: 546 helix: 0.52 (0.33), residues: 248 sheet: 0.32 (0.71), residues: 54 loop : -1.24 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 45 HIS 0.002 0.001 HIS B 52 PHE 0.007 0.001 PHE B 56 TYR 0.023 0.001 TYR A 604 ARG 0.003 0.000 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1266.77 seconds wall clock time: 23 minutes 49.97 seconds (1429.97 seconds total)