Starting phenix.real_space_refine on Mon Jun 24 17:06:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/06_2024/8r4d_18886_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/06_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_18886/06_2024/8r4d_18886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/06_2024/8r4d_18886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/06_2024/8r4d_18886_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4d_18886/06_2024/8r4d_18886_updated.pdb" } 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-5370/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: 2.76, per 1000 atoms: 0.77 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: 1.40 Conformation dependent library (CDL) restraints added in 608.0 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... running ksdssp... Secondary structure from input PDB file: 15 helices and 5 sheets defined 25.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 549 through 557 Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 630 through 643 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 698 through 709 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) Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 750 through 762 Processing helix chain 'A' and resid 810 through 813 No H-bonds generated for 'chain 'A' and resid 810 through 813' Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 563 through 568 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: 6.212A pdb=" N LEU A 510 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 455 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS A 512 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 457 " --> pdb=" O HIS A 512 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP A 514 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 799 through 802 Processing sheet with id= C, 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) Processing sheet with id= D, first strand: chain 'B' and resid 17 through 23 Processing sheet with id= E, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.832A pdb=" N GLU B 46 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 1.52 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: 974 2.81 - 3.33: 3356 3.33 - 3.86: 5676 3.86 - 4.38: 6515 4.38 - 4.90: 10915 Nonbonded interactions: 27436 Sorted by model distance: nonbonded pdb=" N GLU A 686 " pdb=" OE1 GLU A 686 " model vdw 2.289 2.520 nonbonded pdb=" O SER A 711 " pdb=" OG SER A 712 " model vdw 2.327 2.440 nonbonded pdb=" OD1 ASP A 460 " pdb=" NE1 TRP A 551 " model vdw 2.328 2.520 nonbonded pdb=" N VAL A 455 " pdb=" O HIS A 512 " model vdw 2.334 2.520 nonbonded pdb=" OG1 THR A 749 " pdb=" OE1 GLU A 752 " model vdw 2.360 2.440 ... (remaining 27431 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: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 1.060 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.310 Find NCS groups from input model: 0.090 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.650 ------------------------------------------------------------------------------- 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= 0.188 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 : 0.416 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: 0.1835 time to fit residues: 17.8335 Evaluate side-chains 71 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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: 2.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3645 Z= 0.324 Angle : 0.701 6.394 4967 Z= 0.369 Chirality : 0.046 0.180 570 Planarity : 0.005 0.039 631 Dihedral : 10.489 118.505 518 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.65 % Favored : 88.70 % Rotamer: Outliers : 2.68 % Allowed : 9.82 % Favored : 87.50 % 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: -2.86 (0.37), residues: 460 helix: -1.39 (0.41), residues: 142 sheet: -0.70 (0.46), residues: 116 loop : -3.02 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 53 HIS 0.009 0.002 HIS A 523 PHE 0.015 0.002 PHE A 588 TYR 0.021 0.002 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 84 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 768 ASP cc_start: 0.5545 (p0) cc_final: 0.5252 (p0) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.1957 time to fit residues: 17.8698 Evaluate side-chains 79 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 643 THR Chi-restraints excluded: chain A residue 650 ASN 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: 0.7980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.1380 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= 0.218 Angle : 0.603 6.386 4967 Z= 0.316 Chirality : 0.043 0.147 570 Planarity : 0.004 0.038 631 Dihedral : 10.113 118.075 518 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.43 % Favored : 88.91 % Rotamer: Outliers : 3.57 % Allowed : 12.50 % Favored : 83.93 % 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: -2.79 (0.37), residues: 460 helix: -1.24 (0.41), residues: 142 sheet: -0.57 (0.47), residues: 111 loop : -3.07 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.005 0.001 HIS A 523 PHE 0.011 0.001 PHE A 588 TYR 0.009 0.001 TYR A 648 ARG 0.004 0.001 ARG A 824 *********************** 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 89 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.6435 (p0) cc_final: 0.6210 (p0) REVERT: A 760 MET cc_start: 0.7027 (mtm) cc_final: 0.6534 (mtp) outliers start: 12 outliers final: 11 residues processed: 83 average time/residue: 0.1823 time to fit residues: 18.1389 Evaluate side-chains 85 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 TYR 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: 0.6980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3645 Z= 0.289 Angle : 0.653 6.279 4967 Z= 0.344 Chirality : 0.045 0.156 570 Planarity : 0.004 0.039 631 Dihedral : 10.567 123.243 518 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.87 % Favored : 88.48 % Rotamer: Outliers : 4.46 % Allowed : 16.96 % Favored : 78.57 % 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: -2.81 (0.37), residues: 460 helix: -1.38 (0.41), residues: 142 sheet: -0.63 (0.47), residues: 111 loop : -2.95 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 53 HIS 0.006 0.002 HIS A 526 PHE 0.014 0.002 PHE A 588 TYR 0.013 0.002 TYR A 536 ARG 0.003 0.001 ARG A 651 *********************** 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 90 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 556 GLU cc_start: 0.6489 (tp30) cc_final: 0.6242 (tp30) REVERT: A 707 ARG cc_start: 0.6305 (mmm-85) cc_final: 0.6087 (mmm-85) REVERT: A 760 MET cc_start: 0.7355 (mtm) cc_final: 0.6798 (mtp) REVERT: B 86 MET cc_start: 0.6701 (mmm) cc_final: 0.6299 (mtp) outliers start: 15 outliers final: 14 residues processed: 82 average time/residue: 0.1880 time to fit residues: 18.5042 Evaluate side-chains 86 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 TYR 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: 0.8980 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.1771 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= 0.219 Angle : 0.607 6.329 4967 Z= 0.318 Chirality : 0.043 0.146 570 Planarity : 0.004 0.038 631 Dihedral : 10.219 121.864 518 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.43 % Favored : 88.91 % Rotamer: Outliers : 5.36 % Allowed : 18.15 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.37), residues: 460 helix: -1.21 (0.41), residues: 141 sheet: -0.33 (0.47), residues: 103 loop : -2.95 (0.40), residues: 216 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 0.011 0.001 PHE A 588 TYR 0.026 0.002 TYR A 767 ARG 0.004 0.001 ARG A 754 *********************** 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 91 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 760 MET cc_start: 0.7082 (mtm) cc_final: 0.6590 (mtp) REVERT: B 86 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6232 (mtp) outliers start: 18 outliers final: 15 residues processed: 80 average time/residue: 0.1818 time to fit residues: 17.5504 Evaluate side-chains 87 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain B residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.0570 chunk 23 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.1708 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= 0.192 Angle : 0.603 6.826 4967 Z= 0.311 Chirality : 0.043 0.146 570 Planarity : 0.004 0.037 631 Dihedral : 9.820 116.671 518 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.43 % Favored : 88.91 % 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: -2.53 (0.37), residues: 460 helix: -0.92 (0.43), residues: 136 sheet: -0.44 (0.47), residues: 111 loop : -2.94 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 53 HIS 0.003 0.001 HIS A 526 PHE 0.009 0.001 PHE A 588 TYR 0.009 0.001 TYR A 648 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 87 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 760 MET cc_start: 0.7024 (mtm) cc_final: 0.6544 (mtp) REVERT: A 824 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.5976 (mmm-85) REVERT: A 831 MET cc_start: 0.6201 (ptp) cc_final: 0.5712 (ptp) REVERT: B 86 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6233 (mtp) outliers start: 16 outliers final: 12 residues processed: 78 average time/residue: 0.1818 time to fit residues: 17.1748 Evaluate side-chains 81 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 708 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.1864 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= 0.219 Angle : 0.652 14.674 4967 Z= 0.330 Chirality : 0.044 0.188 570 Planarity : 0.004 0.038 631 Dihedral : 9.881 115.893 518 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.65 % Favored : 88.70 % Rotamer: Outliers : 5.95 % Allowed : 18.45 % 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: -2.50 (0.37), residues: 460 helix: -1.01 (0.43), residues: 136 sheet: -0.33 (0.46), residues: 108 loop : -2.87 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.002 0.001 HIS A 596 PHE 0.011 0.001 PHE A 588 TYR 0.010 0.001 TYR B 114 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 93 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 582 LYS cc_start: 0.7248 (mptt) cc_final: 0.6532 (ttpp) REVERT: A 760 MET cc_start: 0.6999 (mtm) cc_final: 0.6543 (mtp) REVERT: A 824 ARG cc_start: 0.6694 (mmm-85) cc_final: 0.6004 (mmm-85) REVERT: B 86 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6225 (mtp) outliers start: 20 outliers final: 15 residues processed: 83 average time/residue: 0.1693 time to fit residues: 16.9288 Evaluate side-chains 87 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 643 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.1905 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= 0.224 Angle : 0.647 12.520 4967 Z= 0.330 Chirality : 0.044 0.165 570 Planarity : 0.004 0.037 631 Dihedral : 9.890 115.899 518 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.43 % Favored : 88.91 % 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: -2.51 (0.37), residues: 460 helix: -1.05 (0.42), residues: 136 sheet: -0.33 (0.46), residues: 108 loop : -2.86 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.003 0.001 HIS A 526 PHE 0.011 0.001 PHE A 588 TYR 0.010 0.001 TYR B 114 ARG 0.005 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 86 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 456 HIS cc_start: 0.6980 (m90) cc_final: 0.6697 (m90) REVERT: A 760 MET cc_start: 0.7128 (mtm) cc_final: 0.6667 (mtp) REVERT: A 824 ARG cc_start: 0.6707 (mmm-85) cc_final: 0.6007 (mmm-85) REVERT: B 86 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6231 (mtp) outliers start: 15 outliers final: 14 residues processed: 79 average time/residue: 0.1742 time to fit residues: 16.5408 Evaluate side-chains 83 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 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 523 HIS Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 643 THR 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 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: 3.9990 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3645 Z= 0.368 Angle : 0.784 13.713 4967 Z= 0.400 Chirality : 0.048 0.165 570 Planarity : 0.005 0.044 631 Dihedral : 10.869 128.493 516 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.09 % Favored : 88.26 % Rotamer: Outliers : 4.46 % Allowed : 21.73 % Favored : 73.81 % 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: -1.57 (0.40), residues: 141 sheet: -0.67 (0.45), residues: 116 loop : -2.99 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 53 HIS 0.004 0.002 HIS A 718 PHE 0.013 0.002 PHE A 588 TYR 0.026 0.002 TYR A 767 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 88 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 LYS cc_start: 0.7258 (mptt) cc_final: 0.6481 (ttpp) REVERT: A 707 ARG cc_start: 0.6309 (mmm-85) cc_final: 0.5985 (mmm-85) REVERT: A 760 MET cc_start: 0.6970 (mtm) cc_final: 0.6518 (mtp) REVERT: B 86 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6668 (mtp) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 0.1874 time to fit residues: 18.9185 Evaluate side-chains 85 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 643 THR 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 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: 0.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.2132 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= 0.250 Angle : 0.699 12.308 4967 Z= 0.355 Chirality : 0.045 0.144 570 Planarity : 0.004 0.038 631 Dihedral : 10.353 127.200 516 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.00 % Favored : 89.35 % Rotamer: Outliers : 4.17 % Allowed : 22.62 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.37), residues: 460 helix: -1.42 (0.40), residues: 141 sheet: -0.61 (0.46), residues: 116 loop : -2.86 (0.41), residues: 203 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 0.012 0.001 PHE A 588 TYR 0.017 0.002 TYR A 767 ARG 0.004 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 84 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 HIS cc_start: 0.7196 (m90) cc_final: 0.6814 (m90) REVERT: A 582 LYS cc_start: 0.7176 (mptt) cc_final: 0.6927 (mptt) REVERT: A 760 MET cc_start: 0.7011 (mtm) cc_final: 0.6567 (mtp) REVERT: B 86 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6218 (mtp) outliers start: 14 outliers final: 13 residues processed: 78 average time/residue: 0.1837 time to fit residues: 17.2335 Evaluate side-chains 84 residues out of total 421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 643 THR 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 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 6 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.0570 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.194627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.168492 restraints weight = 4704.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.170819 restraints weight = 3535.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.173009 restraints weight = 2874.662| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.2027 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= 0.205 Angle : 0.656 11.563 4967 Z= 0.331 Chirality : 0.044 0.160 570 Planarity : 0.004 0.038 631 Dihedral : 9.745 121.346 516 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.09 % Favored : 88.26 % Rotamer: Outliers : 4.17 % Allowed : 22.62 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.37), residues: 460 helix: -1.09 (0.42), residues: 136 sheet: -0.52 (0.46), residues: 116 loop : -2.78 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 53 HIS 0.002 0.001 HIS A 596 PHE 0.009 0.001 PHE A 588 TYR 0.014 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: 1175.72 seconds wall clock time: 22 minutes 3.08 seconds (1323.08 seconds total)