Starting phenix.real_space_refine on Mon Sep 23 14:01:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/09_2024/7swn_25476_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/09_2024/7swn_25476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/09_2024/7swn_25476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/09_2024/7swn_25476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/09_2024/7swn_25476_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/09_2024/7swn_25476_neut.cif" } resolution = 4.3 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= 0.001 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: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2080 2.51 5 N 554 2.21 5 O 632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Time building chain proxies: 2.60, per 1000 atoms: 0.79 Number of scatterers: 3283 At special positions: 0 Unit cell: (100.65, 70.95, 75.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 632 8.00 N 554 7.00 C 2080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 427.4 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 8.3% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 64 removed outlier: 4.034A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.551A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.319A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.864A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.864A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE H 102 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.398A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA9, first strand: chain 'L' and resid 20 through 23 83 hydrogen bonds defined for protein. 186 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: 0.81 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1043 1.34 - 1.46: 862 1.46 - 1.58: 1442 1.58 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 3367 Sorted by residual: bond pdb=" N VAL H 67 " pdb=" CA VAL H 67 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.22e+00 bond pdb=" N VAL H 89 " pdb=" CA VAL H 89 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.22e-02 6.72e+03 8.12e+00 bond pdb=" N VAL L 104 " pdb=" CA VAL L 104 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.22e-02 6.72e+03 7.79e+00 bond pdb=" N ARG H 71 " pdb=" CA ARG H 71 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.29e-02 6.01e+03 7.54e+00 bond pdb=" N ASN A 450 " pdb=" CA ASN A 450 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 7.12e+00 ... (remaining 3362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 4286 2.01 - 4.02: 250 4.02 - 6.02: 34 6.02 - 8.03: 4 8.03 - 10.04: 3 Bond angle restraints: 4577 Sorted by residual: angle pdb=" N VAL H 89 " pdb=" CA VAL H 89 " pdb=" C VAL H 89 " ideal model delta sigma weight residual 106.88 97.68 9.20 1.52e+00 4.33e-01 3.66e+01 angle pdb=" N PRO L 59 " pdb=" CA PRO L 59 " pdb=" C PRO L 59 " ideal model delta sigma weight residual 111.15 118.00 -6.85 1.58e+00 4.01e-01 1.88e+01 angle pdb=" C ILE L 58 " pdb=" N PRO L 59 " pdb=" CA PRO L 59 " ideal model delta sigma weight residual 119.90 124.22 -4.32 1.02e+00 9.61e-01 1.80e+01 angle pdb=" N SER H 74 " pdb=" CA SER H 74 " pdb=" C SER H 74 " ideal model delta sigma weight residual 112.68 107.38 5.30 1.33e+00 5.65e-01 1.59e+01 angle pdb=" N ARG L 61 " pdb=" CA ARG L 61 " pdb=" C ARG L 61 " ideal model delta sigma weight residual 113.31 105.45 7.86 2.04e+00 2.40e-01 1.48e+01 ... (remaining 4572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 1754 16.34 - 32.68: 182 32.68 - 49.01: 42 49.01 - 65.35: 8 65.35 - 81.69: 4 Dihedral angle restraints: 1990 sinusoidal: 771 harmonic: 1219 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -127.47 41.47 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CA VAL A 401 " pdb=" C VAL A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ALA A 522 " pdb=" C ALA A 522 " pdb=" N THR A 523 " pdb=" CA THR A 523 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 1987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 407 0.072 - 0.144: 78 0.144 - 0.216: 6 0.216 - 0.288: 0 0.288 - 0.360: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL H 89 " pdb=" N VAL H 89 " pdb=" C VAL H 89 " pdb=" CB VAL H 89 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA VAL L 104 " pdb=" N VAL L 104 " pdb=" C VAL L 104 " pdb=" CB VAL L 104 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL A 407 " pdb=" CA VAL A 407 " pdb=" CG1 VAL A 407 " pdb=" CG2 VAL A 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 489 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 100F" 0.023 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" CG PHE H 100F" -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE H 100F" 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE H 100F" 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE H 100F" -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 100F" 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE H 100F" -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 50 " 0.016 2.00e-02 2.50e+03 1.63e-02 6.64e+00 pdb=" CG TRP H 50 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP H 50 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP H 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 50 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 50 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP H 50 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 425 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 426 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.032 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 478 2.74 - 3.28: 3571 3.28 - 3.82: 5496 3.82 - 4.36: 6691 4.36 - 4.90: 10807 Nonbonded interactions: 27043 Sorted by model distance: nonbonded pdb=" O LEU L 4 " pdb=" NE2 GLN L 100 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR A 451 " pdb=" O PHE A 497 " model vdw 2.205 3.040 nonbonded pdb=" O LYS H 12 " pdb=" N SER H 112 " model vdw 2.210 3.120 nonbonded pdb=" O PHE H 63 " pdb=" CG1 VAL H 67 " model vdw 2.238 3.460 nonbonded pdb=" O LYS H 62 " pdb=" NH2 ARG H 66 " model vdw 2.241 3.120 ... (remaining 27038 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: 0.780 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.007 0.069 3367 Z= 0.482 Angle : 1.064 10.040 4577 Z= 0.608 Chirality : 0.058 0.360 492 Planarity : 0.007 0.058 592 Dihedral : 14.582 81.689 1195 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 41.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.88 % Favored : 78.12 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.82 (0.35), residues: 416 helix: -4.85 (0.38), residues: 30 sheet: -2.02 (0.52), residues: 102 loop : -3.75 (0.30), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP H 50 HIS 0.002 0.001 HIS A 519 PHE 0.059 0.005 PHE H 100F TYR 0.038 0.003 TYR L 91 ARG 0.012 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.7819 (tt0) cc_final: 0.7602 (tt0) REVERT: A 424 LYS cc_start: 0.9304 (tttm) cc_final: 0.9070 (tmtt) REVERT: A 436 TRP cc_start: 0.7984 (p-90) cc_final: 0.7682 (p-90) REVERT: H 20 VAL cc_start: 0.8821 (t) cc_final: 0.7589 (t) REVERT: H 35 GLN cc_start: 0.8075 (pt0) cc_final: 0.7730 (pt0) REVERT: H 50 TRP cc_start: 0.7631 (p-90) cc_final: 0.7377 (p-90) REVERT: H 52 VAL cc_start: 0.8910 (t) cc_final: 0.8666 (t) REVERT: H 83 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7959 (tpm170) REVERT: L 77 ARG cc_start: 0.6410 (mmm160) cc_final: 0.4600 (mmt180) REVERT: L 89 GLN cc_start: 0.8116 (tt0) cc_final: 0.7912 (tm-30) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2148 time to fit residues: 24.6372 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3367 Z= 0.240 Angle : 0.790 11.794 4577 Z= 0.406 Chirality : 0.047 0.155 492 Planarity : 0.006 0.050 592 Dihedral : 6.547 20.054 466 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.21 (0.36), residues: 416 helix: -4.57 (0.48), residues: 24 sheet: -1.70 (0.49), residues: 103 loop : -3.30 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 353 HIS 0.001 0.001 HIS H 100C PHE 0.027 0.003 PHE H 100F TYR 0.014 0.002 TYR A 495 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.7945 (tt0) cc_final: 0.7701 (tt0) REVERT: A 454 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8594 (tpp80) REVERT: H 35 GLN cc_start: 0.8232 (pt0) cc_final: 0.7980 (pt0) REVERT: H 80 MET cc_start: 0.7897 (ppp) cc_final: 0.7656 (ppp) REVERT: L 42 GLN cc_start: 0.8832 (mp10) cc_final: 0.8619 (mp10) REVERT: L 77 ARG cc_start: 0.6502 (mmm160) cc_final: 0.4661 (mpt180) REVERT: L 89 GLN cc_start: 0.8293 (tt0) cc_final: 0.8002 (tm-30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2141 time to fit residues: 26.0921 Evaluate side-chains 75 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3367 Z= 0.359 Angle : 0.834 10.191 4577 Z= 0.427 Chirality : 0.047 0.157 492 Planarity : 0.007 0.053 592 Dihedral : 6.846 19.631 466 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.14 % Favored : 84.86 % Rotamer: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.22 (0.36), residues: 416 helix: -4.40 (0.50), residues: 24 sheet: -1.78 (0.49), residues: 100 loop : -3.28 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 436 HIS 0.002 0.001 HIS H 100C PHE 0.026 0.003 PHE A 342 TYR 0.023 0.002 TYR L 91 ARG 0.012 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.6206 (t80) cc_final: 0.5955 (t80) REVERT: A 424 LYS cc_start: 0.9212 (tmtt) cc_final: 0.8812 (tptt) REVERT: H 20 VAL cc_start: 0.8964 (t) cc_final: 0.7397 (t) REVERT: H 35 GLN cc_start: 0.8282 (pt0) cc_final: 0.7966 (pt0) REVERT: H 50 TRP cc_start: 0.8090 (p-90) cc_final: 0.7721 (p-90) REVERT: H 80 MET cc_start: 0.7845 (ppp) cc_final: 0.7613 (ppp) REVERT: H 105 GLN cc_start: 0.8032 (pm20) cc_final: 0.7450 (tp-100) REVERT: L 42 GLN cc_start: 0.8818 (mp10) cc_final: 0.8536 (mp10) REVERT: L 49 TYR cc_start: 0.8055 (p90) cc_final: 0.7672 (p90) REVERT: L 77 ARG cc_start: 0.6773 (mmm160) cc_final: 0.5230 (mpt180) REVERT: L 106 ILE cc_start: 0.7197 (mm) cc_final: 0.6986 (mm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1584 time to fit residues: 17.9042 Evaluate side-chains 68 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 437 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3367 Z= 0.209 Angle : 0.737 9.093 4577 Z= 0.375 Chirality : 0.046 0.167 492 Planarity : 0.006 0.055 592 Dihedral : 6.078 17.515 466 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 0.28 % Allowed : 3.06 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.85 (0.37), residues: 416 helix: -4.26 (0.53), residues: 24 sheet: -1.47 (0.51), residues: 96 loop : -3.02 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.016 0.002 PHE A 342 TYR 0.030 0.002 TYR L 91 ARG 0.005 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 LYS cc_start: 0.9180 (tmtt) cc_final: 0.8787 (tptt) REVERT: A 466 ARG cc_start: 0.7334 (ttp80) cc_final: 0.6658 (ttp80) REVERT: A 472 ILE cc_start: 0.8458 (mm) cc_final: 0.8216 (mm) REVERT: H 20 VAL cc_start: 0.8925 (t) cc_final: 0.7278 (t) REVERT: H 35 GLN cc_start: 0.8335 (pt0) cc_final: 0.8102 (pt0) REVERT: H 80 MET cc_start: 0.7748 (ppp) cc_final: 0.7498 (ppp) REVERT: H 105 GLN cc_start: 0.7859 (pm20) cc_final: 0.7497 (tp-100) REVERT: L 49 TYR cc_start: 0.8207 (p90) cc_final: 0.7707 (p90) REVERT: L 77 ARG cc_start: 0.6294 (mmm160) cc_final: 0.5540 (mpt180) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.1671 time to fit residues: 20.5204 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3367 Z= 0.253 Angle : 0.778 14.164 4577 Z= 0.386 Chirality : 0.047 0.300 492 Planarity : 0.006 0.057 592 Dihedral : 6.014 16.223 466 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.02 (0.37), residues: 416 helix: -4.29 (0.52), residues: 30 sheet: -1.56 (0.50), residues: 96 loop : -3.11 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 436 HIS 0.001 0.001 HIS H 100C PHE 0.017 0.002 PHE A 342 TYR 0.029 0.002 TYR L 91 ARG 0.007 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8665 (tppt) cc_final: 0.8334 (tppt) REVERT: A 424 LYS cc_start: 0.9184 (tmtt) cc_final: 0.8805 (tptt) REVERT: A 471 GLU cc_start: 0.7600 (tp30) cc_final: 0.7302 (mp0) REVERT: H 20 VAL cc_start: 0.8877 (t) cc_final: 0.7341 (t) REVERT: H 35 GLN cc_start: 0.8360 (pt0) cc_final: 0.8083 (pt0) REVERT: H 80 MET cc_start: 0.7782 (ppp) cc_final: 0.7564 (ppp) REVERT: H 105 GLN cc_start: 0.7907 (pm20) cc_final: 0.7410 (tp-100) REVERT: L 49 TYR cc_start: 0.8189 (p90) cc_final: 0.7800 (p90) REVERT: L 77 ARG cc_start: 0.6554 (mmm160) cc_final: 0.5187 (mpt180) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1754 time to fit residues: 20.7346 Evaluate side-chains 66 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3367 Z= 0.280 Angle : 0.782 9.612 4577 Z= 0.394 Chirality : 0.047 0.230 492 Planarity : 0.006 0.062 592 Dihedral : 6.122 17.026 466 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.46 % Favored : 86.54 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.91 (0.37), residues: 416 helix: -4.29 (0.51), residues: 30 sheet: -1.46 (0.51), residues: 97 loop : -3.03 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.017 0.002 PHE A 515 TYR 0.030 0.002 TYR L 91 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8650 (tppt) cc_final: 0.8416 (tppt) REVERT: A 424 LYS cc_start: 0.9202 (tmtt) cc_final: 0.8847 (tptt) REVERT: A 439 ASN cc_start: 0.8359 (m-40) cc_final: 0.8023 (m110) REVERT: A 466 ARG cc_start: 0.7391 (ttp80) cc_final: 0.6846 (ttp80) REVERT: A 471 GLU cc_start: 0.7689 (tp30) cc_final: 0.7366 (mp0) REVERT: A 498 GLN cc_start: 0.7726 (pt0) cc_final: 0.7492 (pt0) REVERT: H 20 VAL cc_start: 0.8888 (t) cc_final: 0.7272 (t) REVERT: H 80 MET cc_start: 0.7777 (ppp) cc_final: 0.7560 (ppp) REVERT: H 105 GLN cc_start: 0.7880 (pm20) cc_final: 0.7466 (tp-100) REVERT: L 49 TYR cc_start: 0.8262 (p90) cc_final: 0.7926 (p90) REVERT: L 77 ARG cc_start: 0.6479 (mmm160) cc_final: 0.5193 (mpt180) REVERT: L 81 GLU cc_start: 0.6149 (pm20) cc_final: 0.5655 (pm20) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1578 time to fit residues: 18.5916 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 0.0980 chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3367 Z= 0.269 Angle : 0.775 9.305 4577 Z= 0.389 Chirality : 0.046 0.174 492 Planarity : 0.006 0.069 592 Dihedral : 6.086 17.518 466 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 0.28 % Allowed : 2.79 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.85 (0.37), residues: 416 helix: -4.23 (0.56), residues: 30 sheet: -1.53 (0.51), residues: 99 loop : -2.96 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.001 0.001 HIS H 100C PHE 0.020 0.002 PHE H 100F TYR 0.025 0.002 TYR L 91 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8555 (tppt) cc_final: 0.8022 (tppt) REVERT: A 424 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8822 (tptt) REVERT: A 471 GLU cc_start: 0.7700 (tp30) cc_final: 0.7361 (mp0) REVERT: H 20 VAL cc_start: 0.8873 (t) cc_final: 0.7281 (t) REVERT: H 80 MET cc_start: 0.7838 (ppp) cc_final: 0.7565 (ppp) REVERT: H 105 GLN cc_start: 0.7825 (pm20) cc_final: 0.7365 (tp-100) REVERT: L 49 TYR cc_start: 0.8206 (p90) cc_final: 0.7896 (p90) REVERT: L 77 ARG cc_start: 0.6439 (mmm160) cc_final: 0.5226 (mpt180) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.1554 time to fit residues: 18.3335 Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3367 Z= 0.215 Angle : 0.798 14.712 4577 Z= 0.395 Chirality : 0.049 0.342 492 Planarity : 0.006 0.069 592 Dihedral : 5.900 16.888 466 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.71 (0.37), residues: 416 helix: -4.21 (0.58), residues: 30 sheet: -1.40 (0.50), residues: 99 loop : -2.86 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.001 0.000 HIS H 100C PHE 0.017 0.002 PHE A 515 TYR 0.029 0.002 TYR H 59 ARG 0.005 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8581 (tppt) cc_final: 0.8016 (tppt) REVERT: A 424 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8819 (tptt) REVERT: A 425 LEU cc_start: 0.9166 (mp) cc_final: 0.8961 (mm) REVERT: A 466 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6814 (ttp80) REVERT: A 471 GLU cc_start: 0.7791 (tp30) cc_final: 0.7407 (mp0) REVERT: H 20 VAL cc_start: 0.8804 (t) cc_final: 0.7328 (t) REVERT: H 80 MET cc_start: 0.7816 (ppp) cc_final: 0.7561 (ppp) REVERT: H 105 GLN cc_start: 0.7780 (pm20) cc_final: 0.7337 (tp-100) REVERT: L 49 TYR cc_start: 0.8193 (p90) cc_final: 0.7850 (p90) REVERT: L 77 ARG cc_start: 0.6360 (mmm160) cc_final: 0.5443 (mpt180) REVERT: L 78 LEU cc_start: 0.6078 (tp) cc_final: 0.5689 (tp) REVERT: L 89 GLN cc_start: 0.8154 (tp40) cc_final: 0.7906 (tp40) REVERT: L 97 THR cc_start: 0.7476 (p) cc_final: 0.7161 (p) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1480 time to fit residues: 19.2430 Evaluate side-chains 79 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3367 Z= 0.236 Angle : 0.809 15.090 4577 Z= 0.398 Chirality : 0.049 0.340 492 Planarity : 0.006 0.072 592 Dihedral : 5.916 20.610 466 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.63 (0.37), residues: 416 helix: -4.17 (0.55), residues: 30 sheet: -1.43 (0.50), residues: 99 loop : -2.76 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 353 HIS 0.001 0.000 HIS H 100C PHE 0.014 0.002 PHE A 342 TYR 0.030 0.003 TYR A 453 ARG 0.004 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 LYS cc_start: 0.9150 (tmtt) cc_final: 0.8757 (tmtt) REVERT: A 471 GLU cc_start: 0.7886 (tp30) cc_final: 0.7471 (mp0) REVERT: H 20 VAL cc_start: 0.8803 (t) cc_final: 0.7366 (t) REVERT: H 80 MET cc_start: 0.7885 (ppp) cc_final: 0.7613 (ppp) REVERT: H 105 GLN cc_start: 0.7604 (pm20) cc_final: 0.7260 (tp-100) REVERT: L 49 TYR cc_start: 0.8112 (p90) cc_final: 0.7799 (p90) REVERT: L 77 ARG cc_start: 0.6209 (mmm160) cc_final: 0.5347 (mpt180) REVERT: L 89 GLN cc_start: 0.8196 (tp40) cc_final: 0.7948 (tp40) REVERT: L 97 THR cc_start: 0.7617 (p) cc_final: 0.7329 (p) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.1499 time to fit residues: 18.7370 Evaluate side-chains 77 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0000 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 0.0020 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN H 3 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3367 Z= 0.205 Angle : 0.795 12.894 4577 Z= 0.392 Chirality : 0.049 0.292 492 Planarity : 0.006 0.075 592 Dihedral : 5.525 20.160 466 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.34 % Favored : 89.42 % Rotamer: Outliers : 0.56 % Allowed : 0.56 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.32 (0.38), residues: 416 helix: -4.24 (0.68), residues: 18 sheet: -1.39 (0.51), residues: 101 loop : -2.55 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 35 HIS 0.001 0.001 HIS H 100C PHE 0.018 0.002 PHE A 486 TYR 0.022 0.002 TYR A 453 ARG 0.006 0.001 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 LYS cc_start: 0.9085 (tmtt) cc_final: 0.8716 (tmtt) REVERT: A 425 LEU cc_start: 0.9108 (mp) cc_final: 0.8859 (mm) REVERT: A 466 ARG cc_start: 0.7069 (ttp80) cc_final: 0.6643 (ttp80) REVERT: A 471 GLU cc_start: 0.8023 (tp30) cc_final: 0.7592 (mp0) REVERT: H 79 TYR cc_start: 0.7968 (m-80) cc_final: 0.7736 (m-80) REVERT: H 80 MET cc_start: 0.7872 (ppp) cc_final: 0.7628 (ppp) REVERT: H 105 GLN cc_start: 0.7587 (pm20) cc_final: 0.7290 (tp-100) REVERT: L 49 TYR cc_start: 0.8002 (p90) cc_final: 0.7563 (p90) REVERT: L 77 ARG cc_start: 0.6133 (mmm160) cc_final: 0.5649 (mpt180) REVERT: L 89 GLN cc_start: 0.8194 (tp40) cc_final: 0.7884 (tp40) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1616 time to fit residues: 20.7159 Evaluate side-chains 78 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 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 = 0.3812 r_free = 0.3812 target = 0.091540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.078769 restraints weight = 15180.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.081250 restraints weight = 9601.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.083020 restraints weight = 6668.443| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3367 Z= 0.192 Angle : 0.786 13.828 4577 Z= 0.388 Chirality : 0.048 0.323 492 Planarity : 0.006 0.080 592 Dihedral : 5.406 20.726 466 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.22 (0.38), residues: 416 helix: -4.22 (0.69), residues: 18 sheet: -1.27 (0.51), residues: 96 loop : -2.48 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 35 HIS 0.001 0.000 HIS H 100C PHE 0.018 0.002 PHE A 486 TYR 0.020 0.002 TYR A 453 ARG 0.005 0.001 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1250.46 seconds wall clock time: 23 minutes 2.28 seconds (1382.28 seconds total)