Mon 24 Dec 00:43:40 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2awa-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:43:45 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.2-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1241 and 0 Target number of residues in the AU: 1241 Target solvent content: 0.6294 Checking the provided sequence file Detected sequence length: 390 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1560 Adjusted target solvent content: 0.53 Input MTZ file: 2awa-3.2-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 94.281 70.854 135.686 90.000 91.232 90.000 Input sequence file: 2awa-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12480 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 135.654 3.200 Wilson plot Bfac: 66.21 28833 reflections ( 96.28 % complete ) and 0 restraints for refining 14005 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3557 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3119 (Rfree = 0.000) for 14005 atoms. Found 125 (125 requested) and removed 139 (62 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.11 Search for helices and strands: 0 residues in 0 chains, 14165 seeds are put forward NCS extension: 0 residues added, 14165 seeds are put forward Round 1: 600 peptides, 121 chains. Longest chain 14 peptides. Score 0.290 Round 2: 761 peptides, 128 chains. Longest chain 15 peptides. Score 0.413 Round 3: 800 peptides, 128 chains. Longest chain 15 peptides. Score 0.446 Round 4: 833 peptides, 135 chains. Longest chain 20 peptides. Score 0.448 Round 5: 835 peptides, 127 chains. Longest chain 18 peptides. Score 0.478 Taking the results from Round 5 Chains 128, Residues 708, Estimated correctness of the model 4.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25813 restraints for refining 11392 atoms. 23079 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2607 (Rfree = 0.000) for 11392 atoms. Found 58 (102 requested) and removed 79 (51 requested) atoms. Cycle 2: After refmac, R = 0.2410 (Rfree = 0.000) for 11225 atoms. Found 38 (102 requested) and removed 71 (51 requested) atoms. Cycle 3: After refmac, R = 0.2373 (Rfree = 0.000) for 11122 atoms. Found 32 (100 requested) and removed 58 (50 requested) atoms. Cycle 4: After refmac, R = 0.2276 (Rfree = 0.000) for 11074 atoms. Found 29 (99 requested) and removed 52 (49 requested) atoms. Cycle 5: After refmac, R = 0.2208 (Rfree = 0.000) for 11029 atoms. Found 29 (99 requested) and removed 62 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 11282 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11300 seeds are put forward Round 1: 747 peptides, 134 chains. Longest chain 17 peptides. Score 0.377 Round 2: 822 peptides, 125 chains. Longest chain 28 peptides. Score 0.475 Round 3: 864 peptides, 131 chains. Longest chain 17 peptides. Score 0.487 Round 4: 863 peptides, 131 chains. Longest chain 16 peptides. Score 0.487 Round 5: 855 peptides, 118 chains. Longest chain 23 peptides. Score 0.525 Taking the results from Round 5 Chains 118, Residues 737, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25519 restraints for refining 11394 atoms. 22689 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2338 (Rfree = 0.000) for 11394 atoms. Found 60 (102 requested) and removed 59 (51 requested) atoms. Cycle 7: After refmac, R = 0.2181 (Rfree = 0.000) for 11343 atoms. Found 25 (102 requested) and removed 54 (51 requested) atoms. Cycle 8: After refmac, R = 0.2104 (Rfree = 0.000) for 11283 atoms. Found 27 (101 requested) and removed 54 (50 requested) atoms. Cycle 9: After refmac, R = 0.2019 (Rfree = 0.000) for 11234 atoms. Found 19 (101 requested) and removed 55 (50 requested) atoms. Cycle 10: After refmac, R = 0.1972 (Rfree = 0.000) for 11186 atoms. Found 20 (100 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 11412 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 11431 seeds are put forward Round 1: 769 peptides, 135 chains. Longest chain 16 peptides. Score 0.393 Round 2: 865 peptides, 137 chains. Longest chain 18 peptides. Score 0.467 Round 3: 869 peptides, 126 chains. Longest chain 21 peptides. Score 0.509 Round 4: 865 peptides, 124 chains. Longest chain 22 peptides. Score 0.512 Round 5: 898 peptides, 128 chains. Longest chain 32 peptides. Score 0.524 Taking the results from Round 5 Chains 130, Residues 770, Estimated correctness of the model 19.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 24793 restraints for refining 11394 atoms. 21729 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2364 (Rfree = 0.000) for 11394 atoms. Found 68 (102 requested) and removed 58 (51 requested) atoms. Cycle 12: After refmac, R = 0.2200 (Rfree = 0.000) for 11348 atoms. Found 28 (102 requested) and removed 52 (51 requested) atoms. Cycle 13: After refmac, R = 0.2147 (Rfree = 0.000) for 11300 atoms. Found 19 (101 requested) and removed 55 (50 requested) atoms. Cycle 14: After refmac, R = 0.2110 (Rfree = 0.000) for 11255 atoms. Found 32 (101 requested) and removed 55 (50 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2075 (Rfree = 0.000) for 11223 atoms. Found 14 (100 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 11433 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 11452 seeds are put forward Round 1: 793 peptides, 139 chains. Longest chain 18 peptides. Score 0.399 Round 2: 854 peptides, 128 chains. Longest chain 28 peptides. Score 0.490 Round 3: 861 peptides, 128 chains. Longest chain 21 peptides. Score 0.495 Round 4: 847 peptides, 125 chains. Longest chain 24 peptides. Score 0.495 Round 5: 836 peptides, 121 chains. Longest chain 17 peptides. Score 0.500 Taking the results from Round 5 Chains 122, Residues 715, Estimated correctness of the model 11.3 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25445 restraints for refining 11393 atoms. 22657 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2355 (Rfree = 0.000) for 11393 atoms. Found 54 (102 requested) and removed 60 (51 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2220 (Rfree = 0.000) for 11342 atoms. Found 18 (102 requested) and removed 58 (51 requested) atoms. Cycle 18: After refmac, R = 0.2189 (Rfree = 0.000) for 11276 atoms. Found 23 (101 requested) and removed 54 (50 requested) atoms. Cycle 19: After refmac, R = 0.2110 (Rfree = 0.000) for 11230 atoms. Found 25 (100 requested) and removed 51 (50 requested) atoms. Cycle 20: After refmac, R = 0.2398 (Rfree = 0.000) for 11197 atoms. Found 76 (100 requested) and removed 56 (50 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 11485 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11502 seeds are put forward Round 1: 786 peptides, 137 chains. Longest chain 16 peptides. Score 0.401 Round 2: 856 peptides, 123 chains. Longest chain 25 peptides. Score 0.509 Round 3: 863 peptides, 115 chains. Longest chain 23 peptides. Score 0.541 Round 4: 859 peptides, 120 chains. Longest chain 24 peptides. Score 0.521 Round 5: 865 peptides, 115 chains. Longest chain 29 peptides. Score 0.542 Taking the results from Round 5 Chains 118, Residues 750, Estimated correctness of the model 24.5 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 24527 restraints for refining 11393 atoms. 21448 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2288 (Rfree = 0.000) for 11393 atoms. Found 71 (102 requested) and removed 65 (51 requested) atoms. Cycle 22: After refmac, R = 0.2094 (Rfree = 0.000) for 11353 atoms. Found 26 (102 requested) and removed 57 (51 requested) atoms. Cycle 23: After refmac, R = 0.2076 (Rfree = 0.000) for 11299 atoms. Found 26 (101 requested) and removed 52 (50 requested) atoms. Cycle 24: After refmac, R = 0.2004 (Rfree = 0.000) for 11257 atoms. Found 15 (101 requested) and removed 50 (50 requested) atoms. Cycle 25: After refmac, R = 0.1931 (Rfree = 0.000) for 11214 atoms. Found 16 (100 requested) and removed 51 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 11417 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 11437 seeds are put forward Round 1: 749 peptides, 132 chains. Longest chain 15 peptides. Score 0.387 Round 2: 831 peptides, 127 chains. Longest chain 20 peptides. Score 0.475 Round 3: 862 peptides, 126 chains. Longest chain 21 peptides. Score 0.503 Round 4: 841 peptides, 117 chains. Longest chain 22 peptides. Score 0.518 Round 5: 838 peptides, 122 chains. Longest chain 20 peptides. Score 0.498 Taking the results from Round 4 Chains 117, Residues 724, Estimated correctness of the model 17.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25147 restraints for refining 11393 atoms. 22368 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2097 (Rfree = 0.000) for 11393 atoms. Found 47 (102 requested) and removed 53 (51 requested) atoms. Cycle 27: After refmac, R = 0.1951 (Rfree = 0.000) for 11369 atoms. Found 22 (102 requested) and removed 53 (51 requested) atoms. Cycle 28: After refmac, R = 0.1902 (Rfree = 0.000) for 11317 atoms. Found 25 (101 requested) and removed 50 (50 requested) atoms. Cycle 29: After refmac, R = 0.1861 (Rfree = 0.000) for 11284 atoms. Found 13 (101 requested) and removed 50 (50 requested) atoms. Cycle 30: After refmac, R = 0.1814 (Rfree = 0.000) for 11236 atoms. Found 10 (100 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 11425 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 11434 seeds are put forward Round 1: 707 peptides, 131 chains. Longest chain 18 peptides. Score 0.352 Round 2: 798 peptides, 123 chains. Longest chain 20 peptides. Score 0.462 Round 3: 811 peptides, 121 chains. Longest chain 26 peptides. Score 0.480 Round 4: 815 peptides, 120 chains. Longest chain 22 peptides. Score 0.487 Round 5: 800 peptides, 124 chains. Longest chain 21 peptides. Score 0.461 Taking the results from Round 4 Chains 120, Residues 695, Estimated correctness of the model 7.1 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25048 restraints for refining 11394 atoms. 22367 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2033 (Rfree = 0.000) for 11394 atoms. Found 52 (102 requested) and removed 54 (51 requested) atoms. Cycle 32: After refmac, R = 0.1943 (Rfree = 0.000) for 11358 atoms. Found 12 (102 requested) and removed 53 (51 requested) atoms. Cycle 33: After refmac, R = 0.1888 (Rfree = 0.000) for 11310 atoms. Found 13 (101 requested) and removed 50 (50 requested) atoms. Cycle 34: After refmac, R = 0.1840 (Rfree = 0.000) for 11263 atoms. Found 15 (101 requested) and removed 50 (50 requested) atoms. Cycle 35: After refmac, R = 0.1800 (Rfree = 0.000) for 11224 atoms. Found 11 (100 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 11406 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 11435 seeds are put forward Round 1: 727 peptides, 128 chains. Longest chain 19 peptides. Score 0.382 Round 2: 799 peptides, 127 chains. Longest chain 15 peptides. Score 0.449 Round 3: 792 peptides, 128 chains. Longest chain 22 peptides. Score 0.439 Round 4: 801 peptides, 125 chains. Longest chain 18 peptides. Score 0.458 Round 5: 794 peptides, 123 chains. Longest chain 26 peptides. Score 0.459 Taking the results from Round 5 Chains 123, Residues 671, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 28833 reflections ( 96.28 % complete ) and 25336 restraints for refining 11394 atoms. 22775 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2058 (Rfree = 0.000) for 11394 atoms. Found 32 (102 requested) and removed 52 (51 requested) atoms. Cycle 37: After refmac, R = 0.1960 (Rfree = 0.000) for 11353 atoms. Found 34 (102 requested) and removed 55 (51 requested) atoms. Cycle 38: After refmac, R = 0.1939 (Rfree = 0.000) for 11321 atoms. Found 19 (101 requested) and removed 50 (50 requested) atoms. Cycle 39: After refmac, R = 0.1889 (Rfree = 0.000) for 11279 atoms. Found 14 (101 requested) and removed 50 (50 requested) atoms. Cycle 40: After refmac, R = 0.1846 (Rfree = 0.000) for 11226 atoms. Found 18 (100 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 11401 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 11423 seeds are put forward Round 1: 655 peptides, 120 chains. Longest chain 14 peptides. Score 0.348 Round 2: 762 peptides, 118 chains. Longest chain 14 peptides. Score 0.451 Round 3: 779 peptides, 122 chains. Longest chain 16 peptides. Score 0.450 Round 4: 795 peptides, 118 chains. Longest chain 27 peptides. Score 0.478 Round 5: 808 peptides, 117 chains. Longest chain 32 peptides. Score 0.492 Taking the results from Round 5 Chains 117, Residues 691, Estimated correctness of the model 8.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 28833 reflections ( 96.28 % complete ) and 25312 restraints for refining 11393 atoms. 22665 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2117 (Rfree = 0.000) for 11393 atoms. Found 61 (102 requested) and removed 54 (51 requested) atoms. Cycle 42: After refmac, R = 0.1958 (Rfree = 0.000) for 11377 atoms. Found 22 (102 requested) and removed 52 (51 requested) atoms. Cycle 43: After refmac, R = 0.1911 (Rfree = 0.000) for 11332 atoms. Found 21 (101 requested) and removed 54 (50 requested) atoms. Cycle 44: After refmac, R = 0.1839 (Rfree = 0.000) for 11280 atoms. Found 24 (101 requested) and removed 50 (50 requested) atoms. Cycle 45: After refmac, R = 0.2080 (Rfree = 0.000) for 11248 atoms. Found 73 (101 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 11462 seeds are put forward NCS extension: 54 residues added (0 deleted due to clashes), 11516 seeds are put forward Round 1: 676 peptides, 125 chains. Longest chain 18 peptides. Score 0.347 Round 2: 759 peptides, 115 chains. Longest chain 24 peptides. Score 0.459 Round 3: 739 peptides, 116 chains. Longest chain 22 peptides. Score 0.439 Round 4: 780 peptides, 121 chains. Longest chain 19 peptides. Score 0.455 Round 5: 767 peptides, 114 chains. Longest chain 25 peptides. Score 0.470 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 115, Residues 653, Estimated correctness of the model 1.4 % 2 chains (17 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2awa-3_warpNtrace.pdb as input Building loops using Loopy2018 115 chains (653 residues) following loop building 2 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 28833 reflections ( 96.28 % complete ) and 25353 restraints for refining 11393 atoms. 22800 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2036 (Rfree = 0.000) for 11393 atoms. Found 0 (102 requested) and removed 51 (51 requested) atoms. Cycle 47: After refmac, R = 0.1957 (Rfree = 0.000) for 11323 atoms. Found 0 (101 requested) and removed 32 (50 requested) atoms. Cycle 48: After refmac, R = 0.2216 (Rfree = 0.000) for 11278 atoms. Found 0 (101 requested) and removed 37 (50 requested) atoms. Cycle 49: After refmac, R = 0.1824 (Rfree = 0.000) for 11229 atoms. Found 0 (100 requested) and removed 24 (50 requested) atoms. Writing output files ... TimeTaking 115.08