Starting phenix.real_space_refine on Thu Jul 18 17:47:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uip_42301/07_2024/8uip_42301.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uip_42301/07_2024/8uip_42301.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/8uip_42301/07_2024/8uip_42301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uip_42301/07_2024/8uip_42301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uip_42301/07_2024/8uip_42301.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uip_42301/07_2024/8uip_42301.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= 0.001 sd= 0.023 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 6 5.16 5 C 1548 2.51 5 N 363 2.21 5 O 399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2316 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Time building chain proxies: 2.18, per 1000 atoms: 0.94 Number of scatterers: 2316 At special positions: 0 Unit cell: (54.45, 58.575, 92.4, 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 6 16.00 O 399 8.00 N 363 7.00 C 1548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 607.5 milliseconds 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 582 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 75.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 54 through 70 removed outlier: 3.559A pdb=" N MET A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 100 removed outlier: 3.601A pdb=" N ILE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 139 removed outlier: 4.229A pdb=" N LYS A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU A 121 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY A 124 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 54 through 70 removed outlier: 3.560A pdb=" N MET B 58 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 100 removed outlier: 3.601A pdb=" N ILE B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 139 removed outlier: 4.230A pdb=" N LYS B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU B 121 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 54 through 70 removed outlier: 3.559A pdb=" N MET C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 100 removed outlier: 3.601A pdb=" N ILE C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 90 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 139 removed outlier: 4.230A pdb=" N LYS C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU C 121 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY C 124 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) 144 hydrogen bonds defined for protein. 432 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: 0.43 Time building geometry restraints manager: 0.84 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: 705 1.34 - 1.46: 342 1.46 - 1.57: 1299 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 2358 Sorted by residual: bond pdb=" N PRO B 72 " pdb=" CA PRO B 72 " ideal model delta sigma weight residual 1.474 1.465 0.009 7.40e-03 1.83e+04 1.41e+00 bond pdb=" N PRO A 72 " pdb=" CA PRO A 72 " ideal model delta sigma weight residual 1.474 1.465 0.009 7.40e-03 1.83e+04 1.37e+00 bond pdb=" N PRO C 72 " pdb=" CA PRO C 72 " ideal model delta sigma weight residual 1.474 1.466 0.008 7.40e-03 1.83e+04 1.32e+00 bond pdb=" N GLY C 95 " pdb=" CA GLY C 95 " ideal model delta sigma weight residual 1.454 1.442 0.012 1.24e-02 6.50e+03 9.50e-01 bond pdb=" CA ASN C 119 " pdb=" C ASN C 119 " ideal model delta sigma weight residual 1.522 1.509 0.014 1.40e-02 5.10e+03 9.38e-01 ... (remaining 2353 not shown) Histogram of bond angle deviations from ideal: 100.48 - 106.66: 51 106.66 - 112.84: 1364 112.84 - 119.02: 589 119.02 - 125.20: 1185 125.20 - 131.38: 21 Bond angle restraints: 3210 Sorted by residual: angle pdb=" C SER B 50 " pdb=" N MET B 51 " pdb=" CA MET B 51 " ideal model delta sigma weight residual 121.54 127.41 -5.87 1.91e+00 2.74e-01 9.44e+00 angle pdb=" C SER A 50 " pdb=" N MET A 51 " pdb=" CA MET A 51 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.20e+00 angle pdb=" C SER C 50 " pdb=" N MET C 51 " pdb=" CA MET C 51 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.19e+00 angle pdb=" C GLU C 69 " pdb=" N GLN C 70 " pdb=" CA GLN C 70 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.81e+00 angle pdb=" C GLU B 69 " pdb=" N GLN B 70 " pdb=" CA GLN B 70 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.79e+00 ... (remaining 3205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1235 17.95 - 35.89: 124 35.89 - 53.84: 39 53.84 - 71.78: 0 71.78 - 89.73: 3 Dihedral angle restraints: 1401 sinusoidal: 510 harmonic: 891 Sorted by residual: dihedral pdb=" CB GLU B 49 " pdb=" CG GLU B 49 " pdb=" CD GLU B 49 " pdb=" OE1 GLU B 49 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 49 " pdb=" CG GLU C 49 " pdb=" CD GLU C 49 " pdb=" OE1 GLU C 49 " ideal model delta sinusoidal sigma weight residual 0.00 89.72 -89.72 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 49 " pdb=" CG GLU A 49 " pdb=" CD GLU A 49 " pdb=" OE1 GLU A 49 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 1398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 174 0.022 - 0.043: 103 0.043 - 0.065: 77 0.065 - 0.087: 42 0.087 - 0.109: 15 Chirality restraints: 411 Sorted by residual: chirality pdb=" CA ASN C 119 " pdb=" N ASN C 119 " pdb=" C ASN C 119 " pdb=" CB ASN C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.95e-01 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.87e-01 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.85e-01 ... (remaining 408 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 71 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 72 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 108 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 109 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 108 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 109 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 109 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 109 " 0.019 5.00e-02 4.00e+02 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 37 2.65 - 3.21: 2589 3.21 - 3.77: 3798 3.77 - 4.34: 5186 4.34 - 4.90: 7439 Nonbonded interactions: 19049 Sorted by model distance: nonbonded pdb=" O ALA C 42 " pdb=" OG SER C 46 " model vdw 2.087 2.440 nonbonded pdb=" O ALA A 42 " pdb=" OG SER A 46 " model vdw 2.087 2.440 nonbonded pdb=" O ALA B 42 " pdb=" OG SER B 46 " model vdw 2.088 2.440 nonbonded pdb=" O PHE B 117 " pdb=" ND2 ASN B 120 " model vdw 2.147 2.520 nonbonded pdb=" O PHE A 117 " pdb=" ND2 ASN A 120 " model vdw 2.148 2.520 ... (remaining 19044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.330 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.660 Find NCS groups from input model: 0.080 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:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 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 : 0.004 0.027 2358 Z= 0.217 Angle : 0.793 8.672 3210 Z= 0.438 Chirality : 0.042 0.109 411 Planarity : 0.005 0.034 390 Dihedral : 16.554 89.725 819 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 25.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.46), residues: 297 helix: -1.15 (0.34), residues: 192 sheet: None (None), residues: 0 loop : -2.41 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 40 PHE 0.016 0.002 PHE B 74 TYR 0.006 0.001 TYR A 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.6897 (t) cc_final: 0.6695 (t) REVERT: A 127 PHE cc_start: 0.7957 (m-10) cc_final: 0.7655 (m-80) REVERT: B 58 MET cc_start: 0.5886 (tmm) cc_final: 0.5575 (tmm) REVERT: B 91 GLN cc_start: 0.8229 (mt0) cc_final: 0.7851 (mt0) REVERT: B 96 VAL cc_start: 0.8465 (m) cc_final: 0.8258 (p) REVERT: B 119 ASN cc_start: 0.6612 (t0) cc_final: 0.6220 (t0) REVERT: C 45 LYS cc_start: 0.6834 (tppt) cc_final: 0.6158 (tppt) REVERT: C 101 LEU cc_start: 0.7762 (mt) cc_final: 0.7418 (mt) REVERT: C 116 ASP cc_start: 0.8281 (m-30) cc_final: 0.8023 (m-30) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1081 time to fit residues: 9.0759 Evaluate side-chains 66 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.0870 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2358 Z= 0.205 Angle : 0.711 8.964 3210 Z= 0.371 Chirality : 0.041 0.131 411 Planarity : 0.004 0.032 390 Dihedral : 5.976 16.045 309 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.47), residues: 297 helix: -1.15 (0.33), residues: 204 sheet: None (None), residues: 0 loop : -2.23 (0.71), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 112 PHE 0.016 0.001 PHE A 127 TYR 0.005 0.001 TYR C 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.8269 (mt0) cc_final: 0.8016 (mt0) REVERT: A 127 PHE cc_start: 0.7902 (m-10) cc_final: 0.7628 (m-80) REVERT: B 91 GLN cc_start: 0.8125 (mt0) cc_final: 0.7752 (mt0) REVERT: B 119 ASN cc_start: 0.6580 (t0) cc_final: 0.6145 (m-40) REVERT: C 45 LYS cc_start: 0.6650 (tppt) cc_final: 0.6162 (tppt) REVERT: C 117 PHE cc_start: 0.8609 (t80) cc_final: 0.8326 (t80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1341 time to fit residues: 9.3530 Evaluate side-chains 52 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.5732 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2358 Z= 0.207 Angle : 0.756 7.772 3210 Z= 0.383 Chirality : 0.043 0.154 411 Planarity : 0.004 0.030 390 Dihedral : 5.968 16.622 309 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 25.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.46), residues: 297 helix: -1.28 (0.32), residues: 210 sheet: None (None), residues: 0 loop : -2.76 (0.71), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 112 PHE 0.013 0.001 PHE C 127 TYR 0.006 0.001 TYR C 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.7769 (mptt) cc_final: 0.7219 (tmmt) REVERT: A 127 PHE cc_start: 0.7931 (m-10) cc_final: 0.7697 (m-10) REVERT: B 58 MET cc_start: 0.6035 (tmm) cc_final: 0.5765 (tmm) REVERT: B 91 GLN cc_start: 0.8195 (mt0) cc_final: 0.7824 (mt0) REVERT: B 115 LEU cc_start: 0.8558 (mp) cc_final: 0.8120 (mp) REVERT: B 119 ASN cc_start: 0.6824 (t0) cc_final: 0.6453 (m-40) REVERT: C 45 LYS cc_start: 0.6840 (tppt) cc_final: 0.6322 (tppt) REVERT: C 117 PHE cc_start: 0.8624 (t80) cc_final: 0.8340 (t80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1281 time to fit residues: 9.4775 Evaluate side-chains 54 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.5775 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2358 Z= 0.221 Angle : 0.770 7.941 3210 Z= 0.402 Chirality : 0.046 0.196 411 Planarity : 0.005 0.032 390 Dihedral : 6.125 18.677 309 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 27.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.46), residues: 297 helix: -1.33 (0.33), residues: 213 sheet: None (None), residues: 0 loop : -2.49 (0.72), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 40 PHE 0.014 0.001 PHE C 127 TYR 0.007 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 GLN cc_start: 0.8081 (mt0) cc_final: 0.7595 (mt0) REVERT: B 115 LEU cc_start: 0.8488 (mp) cc_final: 0.7919 (mp) REVERT: B 119 ASN cc_start: 0.7003 (t0) cc_final: 0.6703 (m-40) REVERT: C 91 GLN cc_start: 0.7806 (mt0) cc_final: 0.7240 (mt0) REVERT: C 117 PHE cc_start: 0.8631 (t80) cc_final: 0.8309 (t80) REVERT: C 127 PHE cc_start: 0.7851 (m-80) cc_final: 0.7534 (m-80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1072 time to fit residues: 7.7629 Evaluate side-chains 51 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.0570 chunk 11 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.0170 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 overall best weight: 0.2434 ------------------------------------------------------------------------------- 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: 0.5638 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2358 Z= 0.175 Angle : 0.717 8.015 3210 Z= 0.351 Chirality : 0.042 0.174 411 Planarity : 0.004 0.033 390 Dihedral : 5.718 18.841 309 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.47), residues: 297 helix: -0.96 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -2.91 (0.70), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 40 PHE 0.013 0.001 PHE C 127 TYR 0.012 0.001 TYR A 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.6074 (tmm) cc_final: 0.5732 (tmm) REVERT: B 91 GLN cc_start: 0.8242 (mt0) cc_final: 0.7713 (mt0) REVERT: B 115 LEU cc_start: 0.8529 (mp) cc_final: 0.8050 (mt) REVERT: B 119 ASN cc_start: 0.7108 (t0) cc_final: 0.6810 (m-40) REVERT: C 117 PHE cc_start: 0.8616 (t80) cc_final: 0.8297 (t80) REVERT: C 127 PHE cc_start: 0.7647 (m-80) cc_final: 0.7332 (m-80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1048 time to fit residues: 7.2986 Evaluate side-chains 51 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.0970 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 0.0060 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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: 0.5647 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2358 Z= 0.183 Angle : 0.702 6.937 3210 Z= 0.348 Chirality : 0.044 0.253 411 Planarity : 0.004 0.035 390 Dihedral : 5.519 17.873 309 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.46), residues: 297 helix: -1.16 (0.32), residues: 213 sheet: None (None), residues: 0 loop : -2.87 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 40 PHE 0.009 0.001 PHE C 127 TYR 0.010 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: B 115 LEU cc_start: 0.8504 (mp) cc_final: 0.8060 (mt) REVERT: C 117 PHE cc_start: 0.8603 (t80) cc_final: 0.8276 (t80) REVERT: C 127 PHE cc_start: 0.7414 (m-80) cc_final: 0.7153 (m-80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1015 time to fit residues: 6.9785 Evaluate side-chains 53 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.5654 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2358 Z= 0.182 Angle : 0.714 8.512 3210 Z= 0.348 Chirality : 0.043 0.215 411 Planarity : 0.005 0.035 390 Dihedral : 5.484 19.440 309 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.47), residues: 297 helix: -0.99 (0.33), residues: 207 sheet: None (None), residues: 0 loop : -2.45 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 40 PHE 0.013 0.001 PHE A 127 TYR 0.006 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 111 LYS cc_start: 0.6078 (ptpp) cc_final: 0.5768 (ptpp) REVERT: C 117 PHE cc_start: 0.8589 (t80) cc_final: 0.8264 (t80) REVERT: C 127 PHE cc_start: 0.7296 (m-80) cc_final: 0.7048 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1072 time to fit residues: 6.9120 Evaluate side-chains 50 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.0020 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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: 0.5616 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2358 Z= 0.173 Angle : 0.708 9.762 3210 Z= 0.342 Chirality : 0.042 0.153 411 Planarity : 0.004 0.037 390 Dihedral : 5.267 19.013 309 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.46), residues: 297 helix: -1.06 (0.33), residues: 216 sheet: None (None), residues: 0 loop : -2.79 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 40 PHE 0.009 0.001 PHE A 127 TYR 0.007 0.001 TYR C 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: C 91 GLN cc_start: 0.7768 (mt0) cc_final: 0.7222 (mt0) REVERT: C 117 PHE cc_start: 0.8570 (t80) cc_final: 0.8252 (t80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1026 time to fit residues: 6.8152 Evaluate side-chains 53 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 overall best weight: 0.5922 ------------------------------------------------------------------------------- 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: 0.5638 moved from start: 0.6942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2358 Z= 0.185 Angle : 0.705 8.455 3210 Z= 0.344 Chirality : 0.042 0.160 411 Planarity : 0.005 0.036 390 Dihedral : 5.294 21.479 309 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.46), residues: 297 helix: -1.11 (0.32), residues: 219 sheet: None (None), residues: 0 loop : -2.92 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 40 PHE 0.013 0.001 PHE A 127 TYR 0.006 0.001 TYR C 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.0413 (mtt) cc_final: 0.0141 (mtm) REVERT: C 91 GLN cc_start: 0.7798 (mt0) cc_final: 0.7284 (mt0) REVERT: C 117 PHE cc_start: 0.8590 (t80) cc_final: 0.8262 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1157 time to fit residues: 6.9632 Evaluate side-chains 50 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.5633 moved from start: 0.7211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2358 Z= 0.180 Angle : 0.730 9.704 3210 Z= 0.347 Chirality : 0.042 0.153 411 Planarity : 0.004 0.029 390 Dihedral : 5.300 21.482 309 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.46), residues: 297 helix: -0.95 (0.32), residues: 219 sheet: None (None), residues: 0 loop : -3.18 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 40 PHE 0.011 0.001 PHE A 127 TYR 0.010 0.001 TYR A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.2959 (tmm) cc_final: 0.2683 (tmm) REVERT: B 51 MET cc_start: 0.0474 (mtt) cc_final: 0.0217 (mtm) REVERT: C 91 GLN cc_start: 0.7726 (mt0) cc_final: 0.7205 (mt0) REVERT: C 117 PHE cc_start: 0.8592 (t80) cc_final: 0.8265 (t80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1145 time to fit residues: 6.6099 Evaluate side-chains 47 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.0570 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5374 r_free = 0.5374 target = 0.286985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.272138 restraints weight = 9737.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5317 r_free = 0.5317 target = 0.273234 restraints weight = 7403.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.274387 restraints weight = 6116.445| |-----------------------------------------------------------------------------| r_work (final): 0.4798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 moved from start: 0.7560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2358 Z= 0.176 Angle : 0.698 8.712 3210 Z= 0.335 Chirality : 0.041 0.123 411 Planarity : 0.004 0.030 390 Dihedral : 5.233 21.411 309 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.46), residues: 297 helix: -0.93 (0.32), residues: 219 sheet: None (None), residues: 0 loop : -3.27 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 40 PHE 0.015 0.001 PHE A 127 TYR 0.007 0.001 TYR C 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 978.38 seconds wall clock time: 22 minutes 2.72 seconds (1322.72 seconds total)