null Sun 23 Dec 22:23:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prv-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prv-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prv-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:18 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/hancs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-hancs/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 191 and 0 Target number of residues in the AU: 191 Target solvent content: 0.6643 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-4.0-parrot-hancs.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: 1 Cell parameters: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.70 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: 44.420 4.000 Wilson plot Bfac: 86.85 2458 reflections ( 97.69 % complete ) and 0 restraints for refining 2711 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3919 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3282 (Rfree = 0.000) for 2711 atoms. Found 3 (12 requested) and removed 104 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.90 Search for helices and strands: 0 residues in 0 chains, 2632 seeds are put forward NCS extension: 0 residues added, 2632 seeds are put forward Round 1: 66 peptides, 16 chains. Longest chain 5 peptides. Score 0.181 Round 2: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.236 Round 3: 81 peptides, 18 chains. Longest chain 8 peptides. Score 0.227 Round 4: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.317 Round 5: 79 peptides, 16 chains. Longest chain 9 peptides. Score 0.268 Taking the results from Round 4 Chains 16, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 5478 restraints for refining 2211 atoms. 5210 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2504 (Rfree = 0.000) for 2211 atoms. Found 6 (10 requested) and removed 16 (5 requested) atoms. Cycle 2: After refmac, R = 0.2171 (Rfree = 0.000) for 2182 atoms. Found 3 (10 requested) and removed 14 (5 requested) atoms. Cycle 3: After refmac, R = 0.2079 (Rfree = 0.000) for 2163 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.1812 (Rfree = 0.000) for 2153 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.1791 (Rfree = 0.000) for 2145 atoms. Found 0 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 2171 seeds are put forward NCS extension: 0 residues added, 2171 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 5 peptides. Score 0.207 Round 2: 93 peptides, 20 chains. Longest chain 6 peptides. Score 0.250 Round 3: 95 peptides, 19 chains. Longest chain 9 peptides. Score 0.288 Round 4: 99 peptides, 20 chains. Longest chain 7 peptides. Score 0.287 Round 5: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.294 Taking the results from Round 5 Chains 19, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 5032 restraints for refining 2089 atoms. 4743 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2277 (Rfree = 0.000) for 2089 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 7: After refmac, R = 0.2056 (Rfree = 0.000) for 2072 atoms. Found 3 (9 requested) and removed 12 (4 requested) atoms. Cycle 8: After refmac, R = 0.1803 (Rfree = 0.000) for 2056 atoms. Found 0 (9 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.1748 (Rfree = 0.000) for 2047 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.1786 (Rfree = 0.000) for 2039 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.99 Search for helices and strands: 0 residues in 0 chains, 2075 seeds are put forward NCS extension: 0 residues added, 2075 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 7 peptides. Score 0.244 Round 2: 103 peptides, 22 chains. Longest chain 7 peptides. Score 0.261 Round 3: 98 peptides, 21 chains. Longest chain 7 peptides. Score 0.256 Round 4: 105 peptides, 20 chains. Longest chain 11 peptides. Score 0.322 Round 5: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 5 Chains 20, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4844 restraints for refining 2067 atoms. 4516 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2326 (Rfree = 0.000) for 2067 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 12: After refmac, R = 0.2080 (Rfree = 0.000) for 2055 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.2075 (Rfree = 0.000) for 2045 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 14: After refmac, R = 0.1680 (Rfree = 0.000) for 2039 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. Cycle 15: After refmac, R = 0.1850 (Rfree = 0.000) for 2030 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.97 Search for helices and strands: 0 residues in 0 chains, 2079 seeds are put forward NCS extension: 0 residues added, 2079 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 6 peptides. Score 0.214 Round 2: 107 peptides, 22 chains. Longest chain 12 peptides. Score 0.284 Round 3: 94 peptides, 20 chains. Longest chain 8 peptides. Score 0.257 Round 4: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.274 Round 5: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.321 Taking the results from Round 5 Chains 17, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4934 restraints for refining 2087 atoms. 4651 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1889 (Rfree = 0.000) for 2087 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 17: After refmac, R = 0.1681 (Rfree = 0.000) for 2074 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.1711 (Rfree = 0.000) for 2065 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 19: After refmac, R = 0.1600 (Rfree = 0.000) for 2062 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.1455 (Rfree = 0.000) for 2058 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2081 seeds are put forward NCS extension: 0 residues added, 2081 seeds are put forward Round 1: 66 peptides, 16 chains. Longest chain 5 peptides. Score 0.181 Round 2: 90 peptides, 18 chains. Longest chain 9 peptides. Score 0.283 Round 3: 74 peptides, 16 chains. Longest chain 6 peptides. Score 0.236 Round 4: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.295 Round 5: 80 peptides, 17 chains. Longest chain 6 peptides. Score 0.247 Taking the results from Round 4 Chains 15, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4780 restraints for refining 2046 atoms. 4539 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1920 (Rfree = 0.000) for 2046 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 22: After refmac, R = 0.1719 (Rfree = 0.000) for 2031 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.1557 (Rfree = 0.000) for 2030 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.1417 (Rfree = 0.000) for 2022 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.1383 (Rfree = 0.000) for 2016 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.96 Search for helices and strands: 0 residues in 0 chains, 2039 seeds are put forward NCS extension: 0 residues added, 2039 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.220 Round 2: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.265 Round 3: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Round 4: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.319 Round 5: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.297 Taking the results from Round 4 Chains 15, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4620 restraints for refining 2023 atoms. 4363 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1781 (Rfree = 0.000) for 2023 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.1643 (Rfree = 0.000) for 2015 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.1605 (Rfree = 0.000) for 2014 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.1577 (Rfree = 0.000) for 2007 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.1416 (Rfree = 0.000) for 2004 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.98 Search for helices and strands: 0 residues in 0 chains, 2022 seeds are put forward NCS extension: 0 residues added, 2022 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 6 peptides. Score 0.226 Round 2: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.249 Round 3: 73 peptides, 14 chains. Longest chain 11 peptides. Score 0.284 Round 4: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.315 Round 5: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 5 Chains 12, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4724 restraints for refining 2044 atoms. 4500 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1600 (Rfree = 0.000) for 2044 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. Cycle 32: After refmac, R = 0.1511 (Rfree = 0.000) for 2038 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.1505 (Rfree = 0.000) for 2035 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.1461 (Rfree = 0.000) for 2030 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1462 (Rfree = 0.000) for 2027 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.99 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward NCS extension: 0 residues added, 2055 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 7 peptides. Score 0.275 Round 2: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.292 Round 3: 63 peptides, 12 chains. Longest chain 7 peptides. Score 0.276 Round 4: 71 peptides, 12 chains. Longest chain 8 peptides. Score 0.327 Round 5: 77 peptides, 13 chains. Longest chain 9 peptides. Score 0.336 Taking the results from Round 5 Chains 13, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4766 restraints for refining 2061 atoms. 4523 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1550 (Rfree = 0.000) for 2061 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 37: After refmac, R = 0.1500 (Rfree = 0.000) for 2051 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.1437 (Rfree = 0.000) for 2044 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.1451 (Rfree = 0.000) for 2041 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.1432 (Rfree = 0.000) for 2036 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 4.04 Search for helices and strands: 0 residues in 0 chains, 2070 seeds are put forward NCS extension: 0 residues added, 2070 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.251 Round 2: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.249 Round 3: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.299 Round 4: 61 peptides, 12 chains. Longest chain 10 peptides. Score 0.263 Round 5: 68 peptides, 12 chains. Longest chain 12 peptides. Score 0.308 Taking the results from Round 5 Chains 12, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4791 restraints for refining 2075 atoms. 4579 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1493 (Rfree = 0.000) for 2075 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 42: After refmac, R = 0.1326 (Rfree = 0.000) for 2069 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.1410 (Rfree = 0.000) for 2065 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.1546 (Rfree = 0.000) for 2066 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.1302 (Rfree = 0.000) for 2061 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.98 Search for helices and strands: 0 residues in 0 chains, 2105 seeds are put forward NCS extension: 0 residues added, 2105 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 9 peptides. Score 0.242 Round 2: 64 peptides, 12 chains. Longest chain 10 peptides. Score 0.283 Round 3: 56 peptides, 11 chains. Longest chain 10 peptides. Score 0.258 Round 4: 56 peptides, 10 chains. Longest chain 12 peptides. Score 0.289 Round 5: 53 peptides, 10 chains. Longest chain 9 peptides. Score 0.268 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2prv-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2458 reflections ( 97.69 % complete ) and 4791 restraints for refining 2062 atoms. 4617 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1424 (Rfree = 0.000) for 2062 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1393 (Rfree = 0.000) for 2054 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1406 (Rfree = 0.000) for 2050 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1372 (Rfree = 0.000) for 2046 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:55:03 GMT 2018 Job finished. TimeTaking 31.93 Used memory is bytes: 9197000