null Sun 23 Dec 22:22:56 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 2pg3-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-3.6-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/2pg3-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-3.6-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 22:23:05 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/2pg3-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-3.6-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 150 and 0 Target number of residues in the AU: 150 Target solvent content: 0.6581 Checking the provided sequence file Detected sequence length: 232 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 232 Adjusted target solvent content: 0.47 Input MTZ file: 2pg3-3.6-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: 92 Cell parameters: 78.154 78.154 77.755 90.000 90.000 90.000 Input sequence file: 2pg3-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1856 target number of atoms Had to go as low as 0.65 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 Loops will be built when appropriate and at the last cycle Resolution range: 27.561 3.600 Wilson plot Bfac: 83.65 3056 reflections ( 99.64 % complete ) and 0 restraints for refining 2069 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3866 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3491 (Rfree = 0.000) for 2069 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.79 Search for helices and strands: 0 residues in 0 chains, 2112 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 5 peptides. Score 0.208 Round 2: 79 peptides, 17 chains. Longest chain 6 peptides. Score 0.256 Round 3: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.284 Round 4: 94 peptides, 16 chains. Longest chain 14 peptides. Score 0.397 Round 5: 92 peptides, 17 chains. Longest chain 7 peptides. Score 0.353 Taking the results from Round 4 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.64 % complete ) and 4048 restraints for refining 1683 atoms. 3721 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3347 (Rfree = 0.000) for 1683 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 2: After refmac, R = 0.3230 (Rfree = 0.000) for 1653 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 3: After refmac, R = 0.3119 (Rfree = 0.000) for 1633 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2638 (Rfree = 0.000) for 1622 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.2922 (Rfree = 0.000) for 1614 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.78 Search for helices and strands: 0 residues in 0 chains, 1660 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.279 Round 2: 93 peptides, 16 chains. Longest chain 14 peptides. Score 0.390 Round 3: 89 peptides, 15 chains. Longest chain 11 peptides. Score 0.392 Round 4: 96 peptides, 16 chains. Longest chain 9 peptides. Score 0.410 Round 5: 96 peptides, 17 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 4 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.64 % complete ) and 3775 restraints for refining 1566 atoms. 3471 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3087 (Rfree = 0.000) for 1566 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 7: After refmac, R = 0.3101 (Rfree = 0.000) for 1557 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2662 (Rfree = 0.000) for 1552 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2704 (Rfree = 0.000) for 1542 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 10: After refmac, R = 0.2512 (Rfree = 0.000) for 1533 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.75 Search for helices and strands: 0 residues in 0 chains, 1587 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 8 peptides. Score 0.264 Round 2: 98 peptides, 18 chains. Longest chain 9 peptides. Score 0.365 Round 3: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.324 Round 4: 110 peptides, 19 chains. Longest chain 12 peptides. Score 0.417 Round 5: 102 peptides, 18 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 4 Chains 19, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.64 % complete ) and 3541 restraints for refining 1553 atoms. 3196 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2838 (Rfree = 0.000) for 1553 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 12: After refmac, R = 0.2626 (Rfree = 0.000) for 1538 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2582 (Rfree = 0.000) for 1531 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2416 (Rfree = 0.000) for 1528 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2334 (Rfree = 0.000) for 1522 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.75 Search for helices and strands: 0 residues in 0 chains, 1588 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.267 Round 2: 90 peptides, 17 chains. Longest chain 7 peptides. Score 0.338 Round 3: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.369 Round 4: 90 peptides, 15 chains. Longest chain 14 peptides. Score 0.399 Round 5: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.381 Taking the results from Round 4 Chains 15, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.64 % complete ) and 3678 restraints for refining 1567 atoms. 3393 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2652 (Rfree = 0.000) for 1567 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.2310 (Rfree = 0.000) for 1562 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.2191 (Rfree = 0.000) for 1558 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2082 (Rfree = 0.000) for 1558 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2196 (Rfree = 0.000) for 1558 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.68 Search for helices and strands: 0 residues in 0 chains, 1623 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 6 peptides. Score 0.224 Round 2: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.359 Round 3: 73 peptides, 15 chains. Longest chain 6 peptides. Score 0.274 Round 4: 75 peptides, 15 chains. Longest chain 6 peptides. Score 0.290 Round 5: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.284 Taking the results from Round 2 Chains 14, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.64 % complete ) and 3795 restraints for refining 1593 atoms. 3545 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2300 (Rfree = 0.000) for 1593 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 22: After refmac, R = 0.2197 (Rfree = 0.000) for 1591 atoms. Found 9 (10 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2043 (Rfree = 0.000) for 1586 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2028 (Rfree = 0.000) for 1579 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.1900 (Rfree = 0.000) for 1577 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.74 Search for helices and strands: 0 residues in 0 chains, 1628 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 6 peptides. Score 0.217 Round 2: 77 peptides, 16 chains. Longest chain 6 peptides. Score 0.273 Round 3: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.257 Round 4: 76 peptides, 16 chains. Longest chain 6 peptides. Score 0.265 Round 5: 77 peptides, 16 chains. Longest chain 6 peptides. Score 0.273 Taking the results from Round 5 Chains 16, Residues 61, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.64 % complete ) and 3782 restraints for refining 1620 atoms. 3539 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2230 (Rfree = 0.000) for 1620 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 27: After refmac, R = 0.2102 (Rfree = 0.000) for 1610 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 28: After refmac, R = 0.1906 (Rfree = 0.000) for 1607 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2005 (Rfree = 0.000) for 1606 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 30: After refmac, R = 0.1842 (Rfree = 0.000) for 1607 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.74 Search for helices and strands: 0 residues in 0 chains, 1648 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 5 peptides. Score 0.216 Round 2: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.326 Round 3: 72 peptides, 15 chains. Longest chain 6 peptides. Score 0.267 Round 4: 82 peptides, 15 chains. Longest chain 8 peptides. Score 0.342 Round 5: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.337 Taking the results from Round 4 Chains 15, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.64 % complete ) and 3721 restraints for refining 1629 atoms. 3468 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2309 (Rfree = 0.000) for 1629 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 32: After refmac, R = 0.2196 (Rfree = 0.000) for 1622 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 33: After refmac, R = 0.2298 (Rfree = 0.000) for 1617 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.2136 (Rfree = 0.000) for 1615 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2053 (Rfree = 0.000) for 1617 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.72 Search for helices and strands: 0 residues in 0 chains, 1677 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 8 peptides. Score 0.241 Round 2: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.273 Round 3: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.320 Round 4: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.292 Round 5: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.313 Taking the results from Round 3 Chains 15, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.64 % complete ) and 3957 restraints for refining 1674 atoms. 3716 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2240 (Rfree = 0.000) for 1674 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 37: After refmac, R = 0.2082 (Rfree = 0.000) for 1669 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.1938 (Rfree = 0.000) for 1667 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.1946 (Rfree = 0.000) for 1664 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.1928 (Rfree = 0.000) for 1662 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.73 Search for helices and strands: 0 residues in 0 chains, 1729 seeds are put forward Round 1: 60 peptides, 14 chains. Longest chain 6 peptides. Score 0.202 Round 2: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.290 Round 3: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.347 Round 4: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.243 Round 5: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.327 Taking the results from Round 3 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.64 % complete ) and 3954 restraints for refining 1683 atoms. 3723 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2171 (Rfree = 0.000) for 1683 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.1948 (Rfree = 0.000) for 1679 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.1878 (Rfree = 0.000) for 1679 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1867 (Rfree = 0.000) for 1682 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.1806 (Rfree = 0.000) for 1684 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.73 Search for helices and strands: 0 residues in 0 chains, 1720 seeds are put forward Round 1: 60 peptides, 14 chains. Longest chain 6 peptides. Score 0.202 Round 2: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.276 Round 3: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.262 Round 4: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.267 Round 5: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.262 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 55, 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 2pg3-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3056 reflections ( 99.64 % complete ) and 4136 restraints for refining 1681 atoms. 3930 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2103 (Rfree = 0.000) for 1681 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2071 (Rfree = 0.000) for 1674 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1939 (Rfree = 0.000) for 1666 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1778 (Rfree = 0.000) for 1659 atoms. Found 0 (10 requested) and removed 3 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:25 GMT 2018 Job finished. TimeTaking 29.49 Used memory is bytes: 6377584