null Sun 23 Dec 23:50:40 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 2nlv-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.8-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/2nlv-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.8-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 ============================================================ Sun 23 Dec 23:50:45 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/2nlv-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.8-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 145 and 0 Target number of residues in the AU: 145 Target solvent content: 0.6436 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 224 Adjusted target solvent content: 0.45 Input MTZ file: 2nlv-3.8-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: 46.793 37.359 63.476 90.000 97.240 90.000 Input sequence file: 2nlv-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1792 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: 29.104 3.800 Wilson plot Bfac: 73.11 2254 reflections ( 99.73 % complete ) and 0 restraints for refining 1981 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3647 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2746 (Rfree = 0.000) for 1981 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 2028 seeds are put forward NCS extension: 0 residues added, 2028 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 6 peptides. Score 0.219 Round 2: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.317 Round 3: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.327 Round 4: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.316 Round 5: 104 peptides, 17 chains. Longest chain 9 peptides. Score 0.449 Taking the results from Round 5 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3859 restraints for refining 1620 atoms. 3528 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2933 (Rfree = 0.000) for 1620 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. Cycle 2: After refmac, R = 0.2832 (Rfree = 0.000) for 1603 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 3: After refmac, R = 0.2766 (Rfree = 0.000) for 1599 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 4: After refmac, R = 0.2790 (Rfree = 0.000) for 1596 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.2753 (Rfree = 0.000) for 1591 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 1642 seeds are put forward NCS extension: 0 residues added, 1642 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.299 Round 2: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.445 Round 3: 119 peptides, 21 chains. Longest chain 9 peptides. Score 0.435 Round 4: 120 peptides, 21 chains. Longest chain 12 peptides. Score 0.442 Round 5: 103 peptides, 18 chains. Longest chain 9 peptides. Score 0.412 Taking the results from Round 2 Chains 19, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3757 restraints for refining 1603 atoms. 3404 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3096 (Rfree = 0.000) for 1603 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 7: After refmac, R = 0.2904 (Rfree = 0.000) for 1601 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 8: After refmac, R = 0.2826 (Rfree = 0.000) for 1595 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.2703 (Rfree = 0.000) for 1592 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2762 (Rfree = 0.000) for 1588 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 1638 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1641 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 6 peptides. Score 0.235 Round 2: 96 peptides, 18 chains. Longest chain 7 peptides. Score 0.362 Round 3: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.398 Round 4: 98 peptides, 16 chains. Longest chain 10 peptides. Score 0.438 Round 5: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.405 Taking the results from Round 4 Chains 16, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3867 restraints for refining 1620 atoms. 3555 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2843 (Rfree = 0.000) for 1620 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.2826 (Rfree = 0.000) for 1615 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.2749 (Rfree = 0.000) for 1611 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.2844 (Rfree = 0.000) for 1607 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2405 (Rfree = 0.000) for 1603 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.72 Search for helices and strands: 0 residues in 0 chains, 1637 seeds are put forward NCS extension: 0 residues added, 1637 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 7 peptides. Score 0.294 Round 2: 106 peptides, 16 chains. Longest chain 17 peptides. Score 0.492 Round 3: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.412 Round 4: 112 peptides, 17 chains. Longest chain 15 peptides. Score 0.502 Round 5: 105 peptides, 16 chains. Longest chain 14 peptides. Score 0.485 Taking the results from Round 4 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3797 restraints for refining 1620 atoms. 3434 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2665 (Rfree = 0.000) for 1620 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 17: After refmac, R = 0.2468 (Rfree = 0.000) for 1612 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.2418 (Rfree = 0.000) for 1604 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2389 (Rfree = 0.000) for 1597 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2370 (Rfree = 0.000) for 1591 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 1641 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 1669 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 8 peptides. Score 0.264 Round 2: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.356 Round 3: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.358 Round 4: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.375 Round 5: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.378 Taking the results from Round 5 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3898 restraints for refining 1620 atoms. 3644 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2774 (Rfree = 0.000) for 1620 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2741 (Rfree = 0.000) for 1620 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2569 (Rfree = 0.000) for 1613 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2481 (Rfree = 0.000) for 1611 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2407 (Rfree = 0.000) for 1608 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 1655 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1658 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 8 peptides. Score 0.252 Round 2: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.343 Round 3: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.417 Round 4: 87 peptides, 16 chains. Longest chain 11 peptides. Score 0.358 Round 5: 94 peptides, 16 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 3 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3877 restraints for refining 1620 atoms. 3577 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2700 (Rfree = 0.000) for 1620 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2396 (Rfree = 0.000) for 1618 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.2322 (Rfree = 0.000) for 1610 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2264 (Rfree = 0.000) for 1608 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2235 (Rfree = 0.000) for 1603 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 1651 seeds are put forward NCS extension: 0 residues added, 1651 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 8 peptides. Score 0.253 Round 2: 75 peptides, 14 chains. Longest chain 12 peptides. Score 0.331 Round 3: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.329 Round 4: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.352 Round 5: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.347 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 ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3981 restraints for refining 1620 atoms. 3728 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2522 (Rfree = 0.000) for 1620 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 32: After refmac, R = 0.2334 (Rfree = 0.000) for 1623 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2305 (Rfree = 0.000) for 1621 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2837 (Rfree = 0.000) for 1615 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2114 (Rfree = 0.000) for 1614 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 1643 seeds are put forward NCS extension: 0 residues added, 1643 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 6 peptides. Score 0.247 Round 2: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.329 Round 3: 87 peptides, 19 chains. Longest chain 6 peptides. Score 0.259 Round 4: 86 peptides, 15 chains. Longest chain 9 peptides. Score 0.383 Round 5: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.368 Taking the results from Round 4 Chains 15, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 3883 restraints for refining 1620 atoms. 3614 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2538 (Rfree = 0.000) for 1620 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2293 (Rfree = 0.000) for 1619 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2253 (Rfree = 0.000) for 1613 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2171 (Rfree = 0.000) for 1613 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2308 (Rfree = 0.000) for 1609 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 1650 seeds are put forward NCS extension: 0 residues added, 1650 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 5 peptides. Score 0.215 Round 2: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.325 Round 3: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.336 Round 4: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.352 Round 5: 74 peptides, 14 chains. Longest chain 11 peptides. Score 0.323 Taking the results from Round 4 Chains 12, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2254 reflections ( 99.73 % complete ) and 4030 restraints for refining 1620 atoms. 3814 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2364 (Rfree = 0.000) for 1620 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2269 (Rfree = 0.000) for 1622 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2252 (Rfree = 0.000) for 1620 atoms. Found 5 (8 requested) and removed 56 (4 requested) atoms. Cycle 44: After refmac, R = 0.2292 (Rfree = 0.000) for 1568 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2146 (Rfree = 0.000) for 1571 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 1621 seeds are put forward NCS extension: 0 residues added, 1621 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 6 peptides. Score 0.203 Round 2: 75 peptides, 14 chains. Longest chain 11 peptides. Score 0.331 Round 3: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.300 Round 4: 89 peptides, 16 chains. Longest chain 10 peptides. Score 0.373 Round 5: 84 peptides, 16 chains. Longest chain 7 peptides. Score 0.335 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 73, 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 2nlv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2254 reflections ( 99.73 % complete ) and 3715 restraints for refining 1588 atoms. 3439 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2681 (Rfree = 0.000) for 1588 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2278 (Rfree = 0.000) for 1583 atoms. Found 0 (8 requested) and removed 3 (4 requested) atoms. Cycle 48: After refmac, R = 0.2673 (Rfree = 0.000) for 1577 atoms. Found 0 (8 requested) and removed 1 (4 requested) atoms. Cycle 49: After refmac, R = 0.2576 (Rfree = 0.000) for 1576 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:13:09 GMT 2018 Job finished. TimeTaking 22.47 Used memory is bytes: 18618544