Starting phenix.real_space_refine on Fri Aug 2 16:34:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/08_2024/8r4d_18886.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/08_2024/8r4d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/08_2024/8r4d_18886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/08_2024/8r4d_18886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/08_2024/8r4d_18886.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/08_2024/8r4d_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 Residue "A ASP 504": "OD1" <-> "OD2" Residue "A ASP 545": "OD1" <-> "OD2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 621": "OD1" <-> "OD2" Residue "A TYR 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 803": "OD1" <-> "OD2" Residue "A TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 2.57, per 1000 atoms: 0.72 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 - 3.50 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=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 654.3 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: 0.40 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: 1.03 Time building geometry restraints manager: 1.55 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: 99.20 - 106.15: 80 106.15 - 113.11: 1990 113.11 - 120.06: 1211 120.06 - 127.01: 1639 127.01 - 133.97: 47 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: 0.210 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.380 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.410 ------------------------------------------------------------------------------- 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 3645 Z= 0.184 Angle : 0.647 6.553 4967 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.537 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: 0.1882 time to fit residues: 18.3383 Evaluate side-chains 71 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3645 Z= 0.197 Angle : 0.603 6.643 4967 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 515 ASP cc_start: 0.6392 (p0) cc_final: 0.6166 (p0) REVERT: A 556 GLU cc_start: 0.5981 (tp30) cc_final: 0.5778 (tp30) REVERT: A 581 GLN cc_start: 0.6644 (pp30) cc_final: 0.6088 (pp30) outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 0.1909 time to fit residues: 17.6985 Evaluate side-chains 74 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.0050 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 38 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.4152 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3645 Z= 0.176 Angle : 0.574 6.644 4967 Z= 0.301 Chirality : 0.042 0.152 570 Planarity : 0.004 0.033 631 Dihedral : 9.276 106.853 518 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.57 % Favored : 89.78 % Rotamer: Outliers : 2.08 % Allowed : 12.80 % Favored : 85.12 % 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: -2.44 (0.37), residues: 460 helix: -0.59 (0.44), residues: 133 sheet: -0.47 (0.47), residues: 111 loop : -3.00 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 53 HIS 0.003 0.001 HIS A 549 PHE 0.009 0.001 PHE A 588 TYR 0.008 0.001 TYR A 648 ARG 0.005 0.001 ARG A 754 *********************** 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 84 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.365 Fit side-chains REVERT: A 515 ASP cc_start: 0.6246 (p0) cc_final: 0.5988 (p0) REVERT: A 582 LYS cc_start: 0.6972 (mptt) cc_final: 0.6493 (ttpp) REVERT: A 760 MET cc_start: 0.6965 (mtm) cc_final: 0.6472 (mtp) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.1975 time to fit residues: 18.2922 Evaluate side-chains 78 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.0070 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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** A 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3645 Z= 0.172 Angle : 0.566 6.641 4967 Z= 0.297 Chirality : 0.042 0.148 570 Planarity : 0.004 0.033 631 Dihedral : 9.171 104.741 518 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.78 % Favored : 89.57 % Rotamer: Outliers : 2.38 % Allowed : 16.37 % Favored : 81.25 % 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: -2.39 (0.38), residues: 460 helix: -0.46 (0.45), residues: 133 sheet: -0.50 (0.47), residues: 111 loop : -3.00 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 53 HIS 0.005 0.001 HIS A 526 PHE 0.009 0.001 PHE A 588 TYR 0.008 0.001 TYR A 648 ARG 0.005 0.001 ARG A 754 *********************** 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 84 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 515 ASP cc_start: 0.6266 (p0) cc_final: 0.5979 (p0) REVERT: A 556 GLU cc_start: 0.6469 (tp30) cc_final: 0.6265 (tp30) REVERT: A 582 LYS cc_start: 0.6943 (mptt) cc_final: 0.6385 (ttpp) REVERT: A 760 MET cc_start: 0.7133 (mtm) cc_final: 0.6743 (mtp) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.1783 time to fit residues: 17.0194 Evaluate side-chains 78 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3645 Z= 0.230 Angle : 0.597 6.565 4967 Z= 0.318 Chirality : 0.043 0.152 570 Planarity : 0.004 0.035 631 Dihedral : 9.625 108.278 518 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.43 % Favored : 88.91 % Rotamer: Outliers : 3.57 % Allowed : 15.77 % 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: -2.54 (0.37), residues: 460 helix: -0.79 (0.43), residues: 135 sheet: -0.40 (0.47), residues: 103 loop : -2.98 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.005 0.001 HIS A 523 PHE 0.012 0.002 PHE A 588 TYR 0.010 0.002 TYR A 767 ARG 0.005 0.001 ARG A 651 *********************** 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 92 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 515 ASP cc_start: 0.6302 (p0) cc_final: 0.6005 (p0) REVERT: A 760 MET cc_start: 0.7230 (mtm) cc_final: 0.6883 (mtp) REVERT: B 86 MET cc_start: 0.6806 (mmm) cc_final: 0.6324 (mtp) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.1826 time to fit residues: 18.6474 Evaluate side-chains 85 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3645 Z= 0.282 Angle : 0.646 6.452 4967 Z= 0.342 Chirality : 0.045 0.152 570 Planarity : 0.004 0.039 631 Dihedral : 10.127 112.952 518 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.52 % Favored : 87.83 % Rotamer: Outliers : 3.87 % Allowed : 18.45 % Favored : 77.68 % 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: -2.85 (0.37), residues: 460 helix: -1.27 (0.40), residues: 143 sheet: -0.76 (0.47), residues: 111 loop : -3.01 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 53 HIS 0.007 0.002 HIS A 523 PHE 0.012 0.002 PHE A 588 TYR 0.013 0.002 TYR A 767 ARG 0.004 0.001 ARG A 651 *********************** 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 91 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.426 Fit side-chains REVERT: A 515 ASP cc_start: 0.6452 (p0) cc_final: 0.6116 (p0) REVERT: A 568 MET cc_start: 0.7502 (mtm) cc_final: 0.7026 (mtm) REVERT: A 760 MET cc_start: 0.7314 (mtm) cc_final: 0.6969 (mtp) REVERT: B 86 MET cc_start: 0.6928 (mmm) cc_final: 0.6527 (mtp) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.1877 time to fit residues: 18.4845 Evaluate side-chains 84 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 B residue 74 SER Chi-restraints excluded: chain B residue 98 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3645 Z= 0.249 Angle : 0.638 6.415 4967 Z= 0.335 Chirality : 0.044 0.146 570 Planarity : 0.004 0.039 631 Dihedral : 10.061 114.358 518 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.09 % Favored : 88.26 % Rotamer: Outliers : 5.06 % Allowed : 17.86 % 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: -2.84 (0.37), residues: 460 helix: -1.27 (0.40), residues: 143 sheet: -0.79 (0.47), residues: 111 loop : -2.98 (0.41), residues: 206 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 0.013 0.001 PHE A 588 TYR 0.011 0.002 TYR A 767 ARG 0.004 0.001 ARG A 651 *********************** 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 95 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.405 Fit side-chains REVERT: A 568 MET cc_start: 0.7468 (mtm) cc_final: 0.7012 (mtm) REVERT: A 582 LYS cc_start: 0.7162 (mptt) cc_final: 0.6366 (ttpp) REVERT: A 760 MET cc_start: 0.7294 (mtm) cc_final: 0.6964 (mtp) REVERT: B 86 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6553 (mtp) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.1840 time to fit residues: 18.9679 Evaluate side-chains 87 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 A residue 821 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 98 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3645 Z= 0.270 Angle : 0.682 10.035 4967 Z= 0.354 Chirality : 0.045 0.148 570 Planarity : 0.004 0.039 631 Dihedral : 10.269 117.414 518 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.09 % Favored : 88.26 % 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: -2.87 (0.37), residues: 460 helix: -1.34 (0.40), residues: 143 sheet: -0.79 (0.47), residues: 111 loop : -2.98 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 53 HIS 0.005 0.001 HIS A 523 PHE 0.013 0.002 PHE A 588 TYR 0.012 0.002 TYR A 767 ARG 0.004 0.001 ARG A 651 *********************** 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 90 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.7496 (mtm) cc_final: 0.7055 (mtm) REVERT: A 582 LYS cc_start: 0.7168 (mptt) cc_final: 0.6355 (ttpp) REVERT: A 760 MET cc_start: 0.7319 (mtm) cc_final: 0.7013 (mtp) REVERT: B 86 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6529 (mtp) outliers start: 15 outliers final: 13 residues processed: 82 average time/residue: 0.1858 time to fit residues: 18.2317 Evaluate side-chains 88 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 650 ASN Chi-restraints excluded: chain A residue 681 ILE 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 39 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 SER 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 39 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3645 Z= 0.284 Angle : 0.719 16.911 4967 Z= 0.364 Chirality : 0.046 0.159 570 Planarity : 0.004 0.039 631 Dihedral : 10.466 121.330 518 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.52 % Favored : 87.83 % Rotamer: Outliers : 4.46 % Allowed : 20.54 % Favored : 75.00 % 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: -2.92 (0.36), residues: 460 helix: -1.36 (0.39), residues: 143 sheet: -0.91 (0.47), residues: 111 loop : -2.96 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 514 HIS 0.004 0.001 HIS A 526 PHE 0.013 0.002 PHE A 588 TYR 0.011 0.002 TYR B 114 ARG 0.004 0.001 ARG A 651 *********************** 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 90 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.7504 (mtm) cc_final: 0.7068 (mtm) REVERT: A 582 LYS cc_start: 0.7141 (mptt) cc_final: 0.6314 (ttpp) REVERT: A 760 MET cc_start: 0.7186 (mtm) cc_final: 0.6839 (mtp) REVERT: B 86 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6635 (mtp) outliers start: 15 outliers final: 13 residues processed: 82 average time/residue: 0.1880 time to fit residues: 18.4278 Evaluate side-chains 88 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 650 ASN Chi-restraints excluded: chain A residue 681 ILE 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 39 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 98 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.0270 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3645 Z= 0.222 Angle : 0.671 16.199 4967 Z= 0.338 Chirality : 0.045 0.164 570 Planarity : 0.004 0.038 631 Dihedral : 10.017 118.160 518 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.65 % Favored : 88.70 % Rotamer: Outliers : 4.76 % Allowed : 20.24 % Favored : 75.00 % 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: -2.74 (0.37), residues: 460 helix: -1.06 (0.41), residues: 141 sheet: -0.82 (0.46), residues: 111 loop : -2.95 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 514 HIS 0.003 0.001 HIS A 526 PHE 0.011 0.001 PHE A 588 TYR 0.011 0.001 TYR A 767 ARG 0.005 0.001 ARG A 651 ********************** 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 93 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 LYS cc_start: 0.7187 (mptt) cc_final: 0.6441 (ttpp) REVERT: A 760 MET cc_start: 0.7128 (mtm) cc_final: 0.6841 (mtp) REVERT: A 824 ARG cc_start: 0.6707 (mmm-85) cc_final: 0.6051 (mmm-85) REVERT: B 86 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6509 (mtp) outliers start: 16 outliers final: 12 residues processed: 85 average time/residue: 0.1871 time to fit residues: 19.0230 Evaluate side-chains 89 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 A residue 821 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 Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 98 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 2 optimal weight: 0.0170 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.198635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172740 restraints weight = 4636.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.174926 restraints weight = 3524.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.176701 restraints weight = 2875.831| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3645 Z= 0.187 Angle : 0.641 15.520 4967 Z= 0.321 Chirality : 0.044 0.150 570 Planarity : 0.004 0.037 631 Dihedral : 9.419 110.546 518 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.43 % Favored : 88.91 % Rotamer: Outliers : 3.87 % Allowed : 20.83 % Favored : 75.30 % 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: -2.49 (0.38), residues: 460 helix: -0.67 (0.44), residues: 135 sheet: -0.83 (0.45), residues: 116 loop : -2.84 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 514 HIS 0.002 0.001 HIS A 526 PHE 0.008 0.001 PHE A 588 TYR 0.011 0.001 TYR A 767 ARG 0.004 0.001 ARG A 651 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1191.50 seconds wall clock time: 21 minutes 43.35 seconds (1303.35 seconds total)