Starting phenix.real_space_refine on Sun Mar 10 16:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/03_2024/7swn_25476_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/03_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_25476/03_2024/7swn_25476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/03_2024/7swn_25476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/03_2024/7swn_25476_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swn_25476/03_2024/7swn_25476_neut.pdb" } 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 Residue "A ARG 346": "NH1" <-> "NH2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.19, per 1000 atoms: 0.67 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 - 3.50 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: 1.41 Conformation dependent library (CDL) restraints added in 654.2 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: 0.48 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: 0.89 Time building geometry restraints manager: 1.53 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: 97.68 - 105.15: 66 105.15 - 112.62: 1676 112.62 - 120.10: 1265 120.10 - 127.57: 1536 127.57 - 135.04: 34 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 2.520 nonbonded pdb=" OH TYR A 451 " pdb=" O PHE A 497 " model vdw 2.205 2.440 nonbonded pdb=" O LYS H 12 " pdb=" N SER H 112 " model vdw 2.210 2.520 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 2.520 ... (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 ========== 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.900 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.900 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- 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 : 0.406 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: 0.2192 time to fit residues: 25.1466 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3367 Z= 0.240 Angle : 0.773 10.244 4577 Z= 0.394 Chirality : 0.047 0.155 492 Planarity : 0.006 0.048 592 Dihedral : 6.408 20.057 466 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % 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: -4.24 (0.36), residues: 416 helix: -4.63 (0.49), residues: 24 sheet: -1.73 (0.50), residues: 99 loop : -3.29 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 101 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.9136 (mm) cc_final: 0.8931 (mm) REVERT: H 35 GLN cc_start: 0.8237 (pt0) cc_final: 0.7994 (pt0) REVERT: H 80 MET cc_start: 0.7940 (ppp) cc_final: 0.7651 (ppp) REVERT: L 77 ARG cc_start: 0.6429 (mmm160) cc_final: 0.4442 (mpt180) REVERT: L 89 GLN cc_start: 0.8427 (tt0) cc_final: 0.8030 (tm-30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2109 time to fit residues: 24.8930 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 9.9990 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 0.0980 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3367 Z= 0.230 Angle : 0.755 9.884 4577 Z= 0.378 Chirality : 0.048 0.249 492 Planarity : 0.006 0.044 592 Dihedral : 5.923 19.539 466 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 0.28 % Allowed : 6.69 % Favored : 93.04 % 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: -4.24 (0.36), residues: 416 helix: -4.56 (0.44), residues: 30 sheet: -1.50 (0.51), residues: 96 loop : -3.34 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 436 HIS 0.002 0.001 HIS H 100C PHE 0.019 0.002 PHE A 342 TYR 0.032 0.002 TYR L 49 ARG 0.010 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 99 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 LYS cc_start: 0.9128 (tmtt) cc_final: 0.8746 (tmtt) REVERT: A 466 ARG cc_start: 0.7587 (ttp80) cc_final: 0.6950 (ttp80) REVERT: A 471 GLU cc_start: 0.7729 (mp0) cc_final: 0.7477 (mp0) REVERT: H 35 GLN cc_start: 0.8279 (pt0) cc_final: 0.7996 (pt0) REVERT: H 80 MET cc_start: 0.7947 (ppp) cc_final: 0.7678 (ppp) REVERT: L 42 GLN cc_start: 0.8774 (mp10) cc_final: 0.8422 (mp10) REVERT: L 77 ARG cc_start: 0.6652 (mmm160) cc_final: 0.4911 (mpt180) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1817 time to fit residues: 21.2420 Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 0.1980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 overall best weight: 1.4122 ------------------------------------------------------------------------------- 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 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3367 Z= 0.211 Angle : 0.743 11.426 4577 Z= 0.373 Chirality : 0.048 0.267 492 Planarity : 0.006 0.044 592 Dihedral : 5.694 20.807 466 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 0.28 % Allowed : 4.18 % Favored : 95.54 % 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: -4.12 (0.36), residues: 416 helix: -4.41 (0.49), residues: 30 sheet: -1.60 (0.49), residues: 100 loop : -3.20 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.017 0.002 PHE A 342 TYR 0.032 0.002 TYR L 91 ARG 0.004 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 105 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.375 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: 0.9077 (tmtt) cc_final: 0.8769 (tptt) REVERT: A 466 ARG cc_start: 0.7274 (ttp80) cc_final: 0.6661 (ttp80) REVERT: A 471 GLU cc_start: 0.7649 (mp0) cc_final: 0.7412 (mp0) REVERT: H 20 VAL cc_start: 0.8808 (t) cc_final: 0.8377 (t) REVERT: H 35 GLN cc_start: 0.8323 (pt0) cc_final: 0.8019 (pt0) REVERT: H 105 GLN cc_start: 0.7985 (pm20) cc_final: 0.7331 (tp-100) REVERT: L 42 GLN cc_start: 0.8766 (mp10) cc_final: 0.8460 (mp10) REVERT: L 77 ARG cc_start: 0.6265 (mmm160) cc_final: 0.4774 (mpt180) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.1740 time to fit residues: 21.6166 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.0070 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.0370 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3367 Z= 0.176 Angle : 0.697 8.873 4577 Z= 0.345 Chirality : 0.045 0.181 492 Planarity : 0.005 0.043 592 Dihedral : 5.224 16.547 466 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % 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: -3.98 (0.36), residues: 416 helix: -4.29 (0.54), residues: 30 sheet: -1.72 (0.46), residues: 110 loop : -3.03 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 436 HIS 0.001 0.000 HIS H 100C PHE 0.015 0.002 PHE A 342 TYR 0.017 0.002 TYR L 91 ARG 0.004 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 107 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.412 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: 0.9050 (tmtt) cc_final: 0.8662 (tmtt) REVERT: A 466 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6594 (ttp80) REVERT: A 471 GLU cc_start: 0.7629 (mp0) cc_final: 0.7332 (mp0) REVERT: A 492 LEU cc_start: 0.8816 (mm) cc_final: 0.8558 (mm) REVERT: H 35 GLN cc_start: 0.8364 (pt0) cc_final: 0.7832 (pt0) REVERT: H 105 GLN cc_start: 0.7953 (pm20) cc_final: 0.7295 (tp-100) REVERT: H 108 MET cc_start: 0.8336 (mtt) cc_final: 0.7989 (mtp) REVERT: L 49 TYR cc_start: 0.7950 (p90) cc_final: 0.7709 (p90) REVERT: L 77 ARG cc_start: 0.6309 (mmm160) cc_final: 0.5005 (mpt180) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1735 time to fit residues: 22.2300 Evaluate side-chains 78 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 0.6980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 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 : 0.003 0.041 3367 Z= 0.204 Angle : 0.730 13.561 4577 Z= 0.357 Chirality : 0.047 0.313 492 Planarity : 0.005 0.049 592 Dihedral : 5.295 15.859 466 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % 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: -3.72 (0.37), residues: 416 helix: -4.24 (0.55), residues: 30 sheet: -1.23 (0.48), residues: 100 loop : -2.94 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 353 HIS 0.002 0.001 HIS H 100C PHE 0.026 0.002 PHE H 100F TYR 0.025 0.002 TYR A 453 ARG 0.004 0.001 ARG L 77 *********************** 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 94 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8590 (tptt) cc_final: 0.8357 (ptmt) REVERT: A 424 LYS cc_start: 0.9068 (tmtt) cc_final: 0.8695 (tmtt) REVERT: A 471 GLU cc_start: 0.7686 (mp0) cc_final: 0.7363 (mp0) REVERT: H 105 GLN cc_start: 0.7934 (pm20) cc_final: 0.7281 (tp-100) REVERT: H 108 MET cc_start: 0.8291 (mtt) cc_final: 0.8069 (mtp) REVERT: L 77 ARG cc_start: 0.6371 (mmm160) cc_final: 0.4858 (mpt180) REVERT: L 78 LEU cc_start: 0.5551 (tp) cc_final: 0.5305 (tp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1816 time to fit residues: 20.2301 Evaluate side-chains 75 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 0.0670 chunk 25 optimal weight: 3.9990 overall best weight: 1.8122 ------------------------------------------------------------------------------- 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: 0.6923 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3367 Z= 0.237 Angle : 0.762 13.600 4577 Z= 0.376 Chirality : 0.047 0.323 492 Planarity : 0.006 0.048 592 Dihedral : 5.448 15.800 466 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -3.58 (0.37), residues: 416 helix: -4.31 (0.54), residues: 30 sheet: -1.10 (0.51), residues: 97 loop : -2.82 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 353 HIS 0.001 0.001 HIS H 100C PHE 0.017 0.002 PHE H 100F TYR 0.017 0.002 TYR L 91 ARG 0.008 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 91 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7076 (m-30) cc_final: 0.6625 (m-30) REVERT: A 417 LYS cc_start: 0.8603 (tptt) cc_final: 0.7974 (tppt) REVERT: A 424 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8729 (tmtt) REVERT: A 471 GLU cc_start: 0.7768 (mp0) cc_final: 0.7415 (mp0) REVERT: A 516 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8274 (mp0) REVERT: H 80 MET cc_start: 0.7591 (ppp) cc_final: 0.7371 (ppp) REVERT: H 105 GLN cc_start: 0.7780 (pm20) cc_final: 0.7256 (tp-100) REVERT: H 108 MET cc_start: 0.8261 (mtt) cc_final: 0.8018 (mtp) REVERT: L 77 ARG cc_start: 0.6442 (mmm160) cc_final: 0.5075 (mpt180) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1592 time to fit residues: 17.5177 Evaluate side-chains 76 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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: 0.6977 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3367 Z= 0.275 Angle : 0.787 14.091 4577 Z= 0.391 Chirality : 0.048 0.320 492 Planarity : 0.006 0.048 592 Dihedral : 5.774 18.361 466 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 30.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % 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: -3.52 (0.37), residues: 416 helix: -4.36 (0.48), residues: 30 sheet: -1.05 (0.52), residues: 97 loop : -2.78 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 353 HIS 0.001 0.001 HIS H 100C PHE 0.019 0.002 PHE H 100F TYR 0.016 0.002 TYR L 49 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 89 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7333 (m-30) cc_final: 0.6914 (m-30) REVERT: A 424 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8752 (tmtt) REVERT: A 471 GLU cc_start: 0.7785 (mp0) cc_final: 0.7435 (mp0) REVERT: H 80 MET cc_start: 0.7728 (ppp) cc_final: 0.7443 (ppp) REVERT: H 105 GLN cc_start: 0.7746 (pm20) cc_final: 0.7153 (tp-100) REVERT: H 108 MET cc_start: 0.8232 (mtt) cc_final: 0.8032 (mtp) REVERT: L 77 ARG cc_start: 0.6211 (mmm160) cc_final: 0.4841 (mpt180) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1596 time to fit residues: 17.1928 Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3367 Z= 0.269 Angle : 0.798 14.899 4577 Z= 0.395 Chirality : 0.049 0.334 492 Planarity : 0.006 0.047 592 Dihedral : 5.877 18.307 466 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 31.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 0.28 % Allowed : 0.84 % 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: -3.55 (0.37), residues: 416 helix: -4.46 (0.42), residues: 30 sheet: -1.03 (0.53), residues: 97 loop : -2.80 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 353 HIS 0.002 0.001 HIS H 100C PHE 0.018 0.002 PHE H 100F TYR 0.033 0.002 TYR H 59 ARG 0.006 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 94 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7173 (m-30) cc_final: 0.6769 (m-30) REVERT: A 417 LYS cc_start: 0.8600 (tptt) cc_final: 0.8011 (tppt) REVERT: A 424 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8760 (tmtt) REVERT: A 471 GLU cc_start: 0.7823 (mp0) cc_final: 0.7449 (mp0) REVERT: A 516 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8167 (mp0) REVERT: H 20 VAL cc_start: 0.8995 (t) cc_final: 0.7644 (t) REVERT: H 80 MET cc_start: 0.7544 (ppp) cc_final: 0.7311 (ppp) REVERT: H 105 GLN cc_start: 0.7677 (pm20) cc_final: 0.7165 (tp-100) REVERT: H 108 MET cc_start: 0.8267 (mtt) cc_final: 0.7951 (mtp) REVERT: L 77 ARG cc_start: 0.6128 (mmm160) cc_final: 0.4842 (mpt180) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1621 time to fit residues: 18.2188 Evaluate side-chains 69 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 10.0000 chunk 3 optimal weight: 0.4980 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 493 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3367 Z= 0.199 Angle : 0.754 14.166 4577 Z= 0.368 Chirality : 0.048 0.327 492 Planarity : 0.005 0.049 592 Dihedral : 5.430 17.388 466 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 0.28 % Allowed : 1.11 % 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: -3.38 (0.38), residues: 416 helix: -4.34 (0.48), residues: 30 sheet: -0.93 (0.55), residues: 97 loop : -2.68 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 353 HIS 0.001 0.000 HIS H 100C PHE 0.018 0.002 PHE A 486 TYR 0.016 0.002 TYR L 91 ARG 0.008 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 97 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7153 (m-30) cc_final: 0.6703 (m-30) REVERT: A 417 LYS cc_start: 0.8606 (tptt) cc_final: 0.7993 (tppt) REVERT: A 424 LYS cc_start: 0.9119 (tmtt) cc_final: 0.8832 (tptt) REVERT: A 471 GLU cc_start: 0.7751 (mp0) cc_final: 0.7372 (mp0) REVERT: H 73 MET cc_start: 0.7114 (mmp) cc_final: 0.6906 (mmt) REVERT: H 105 GLN cc_start: 0.7570 (pm20) cc_final: 0.7172 (tp-100) REVERT: L 77 ARG cc_start: 0.6004 (mmm160) cc_final: 0.4950 (mpt180) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1565 time to fit residues: 18.4663 Evaluate side-chains 74 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.089564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.076914 restraints weight = 15247.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.079343 restraints weight = 9634.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.081147 restraints weight = 6716.828| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3367 Z= 0.214 Angle : 0.767 15.620 4577 Z= 0.377 Chirality : 0.048 0.368 492 Planarity : 0.006 0.049 592 Dihedral : 5.498 20.344 466 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.28 % Allowed : 0.00 % Favored : 99.72 % 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: -3.36 (0.39), residues: 416 helix: -4.41 (0.46), residues: 30 sheet: -1.06 (0.52), residues: 106 loop : -2.62 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 353 HIS 0.001 0.000 HIS H 100C PHE 0.015 0.002 PHE H 100F TYR 0.016 0.002 TYR H 59 ARG 0.007 0.001 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1256.69 seconds wall clock time: 23 minutes 18.22 seconds (1398.22 seconds total)