Mon 24 Dec 07:35:44 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fqp-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-noncs ############### 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 07:35:48 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/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.6-parrot-noncs/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 232 and 0 Target number of residues in the AU: 232 Target solvent content: 0.6292 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-3.6-parrot-noncs.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: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3104 target number of atoms Had to go as low as 0.60 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: 50.895 3.601 Wilson plot Bfac: 65.51 3216 reflections ( 82.48 % complete ) and 0 restraints for refining 3425 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3250 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2904 (Rfree = 0.000) for 3425 atoms. Found 18 (21 requested) and removed 135 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.81 Search for helices and strands: 0 residues in 0 chains, 3340 seeds are put forward NCS extension: 0 residues added, 3340 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 7 peptides. Score 0.239 Round 2: 115 peptides, 22 chains. Longest chain 9 peptides. Score 0.319 Round 3: 124 peptides, 22 chains. Longest chain 16 peptides. Score 0.365 Round 4: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.350 Round 5: 126 peptides, 23 chains. Longest chain 11 peptides. Score 0.353 Taking the results from Round 3 Chains 22, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6827 restraints for refining 2813 atoms. 6441 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2175 (Rfree = 0.000) for 2813 atoms. Found 14 (18 requested) and removed 19 (9 requested) atoms. Cycle 2: After refmac, R = 0.2150 (Rfree = 0.000) for 2772 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 3: After refmac, R = 0.1918 (Rfree = 0.000) for 2762 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.1826 (Rfree = 0.000) for 2748 atoms. Found 16 (17 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.1462 (Rfree = 0.000) for 2745 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.87 Search for helices and strands: 0 residues in 0 chains, 2797 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2811 seeds are put forward Round 1: 118 peptides, 25 chains. Longest chain 7 peptides. Score 0.268 Round 2: 149 peptides, 27 chains. Longest chain 12 peptides. Score 0.382 Round 3: 152 peptides, 28 chains. Longest chain 15 peptides. Score 0.376 Round 4: 157 peptides, 28 chains. Longest chain 14 peptides. Score 0.400 Round 5: 163 peptides, 29 chains. Longest chain 15 peptides. Score 0.408 Taking the results from Round 5 Chains 29, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6387 restraints for refining 2668 atoms. 5880 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1776 (Rfree = 0.000) for 2668 atoms. Found 13 (17 requested) and removed 15 (8 requested) atoms. Cycle 7: After refmac, R = 0.1579 (Rfree = 0.000) for 2649 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.1652 (Rfree = 0.000) for 2633 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.1382 (Rfree = 0.000) for 2622 atoms. Found 1 (16 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.1364 (Rfree = 0.000) for 2607 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.81 Search for helices and strands: 0 residues in 0 chains, 2641 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2660 seeds are put forward Round 1: 136 peptides, 26 chains. Longest chain 13 peptides. Score 0.339 Round 2: 158 peptides, 30 chains. Longest chain 13 peptides. Score 0.365 Round 3: 166 peptides, 30 chains. Longest chain 10 peptides. Score 0.402 Round 4: 166 peptides, 29 chains. Longest chain 16 peptides. Score 0.422 Round 5: 152 peptides, 28 chains. Longest chain 9 peptides. Score 0.376 Taking the results from Round 4 Chains 29, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6143 restraints for refining 2657 atoms. 5624 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1642 (Rfree = 0.000) for 2657 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 12: After refmac, R = 0.1465 (Rfree = 0.000) for 2641 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 13: After refmac, R = 0.1402 (Rfree = 0.000) for 2628 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.1290 (Rfree = 0.000) for 2616 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.1291 (Rfree = 0.000) for 2603 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.87 Search for helices and strands: 0 residues in 0 chains, 2663 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 2690 seeds are put forward Round 1: 126 peptides, 29 chains. Longest chain 7 peptides. Score 0.222 Round 2: 143 peptides, 26 chains. Longest chain 12 peptides. Score 0.374 Round 3: 147 peptides, 26 chains. Longest chain 13 peptides. Score 0.393 Round 4: 156 peptides, 28 chains. Longest chain 10 peptides. Score 0.395 Round 5: 148 peptides, 26 chains. Longest chain 10 peptides. Score 0.398 Taking the results from Round 5 Chains 26, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6132 restraints for refining 2601 atoms. 5670 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1453 (Rfree = 0.000) for 2601 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.1546 (Rfree = 0.000) for 2588 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.1539 (Rfree = 0.000) for 2581 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.1137 (Rfree = 0.000) for 2572 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.1208 (Rfree = 0.000) for 2566 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.80 Search for helices and strands: 0 residues in 0 chains, 2600 seeds are put forward NCS extension: 0 residues added, 2600 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 8 peptides. Score 0.278 Round 2: 136 peptides, 24 chains. Longest chain 18 peptides. Score 0.381 Round 3: 134 peptides, 21 chains. Longest chain 15 peptides. Score 0.434 Round 4: 135 peptides, 21 chains. Longest chain 20 peptides. Score 0.438 Round 5: 133 peptides, 19 chains. Longest chain 16 peptides. Score 0.469 Taking the results from Round 5 Chains 19, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6045 restraints for refining 2598 atoms. 5608 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1551 (Rfree = 0.000) for 2598 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. Cycle 22: After refmac, R = 0.1520 (Rfree = 0.000) for 2590 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.1180 (Rfree = 0.000) for 2584 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1255 (Rfree = 0.000) for 2572 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.1526 (Rfree = 0.000) for 2559 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.80 Search for helices and strands: 0 residues in 0 chains, 2620 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2646 seeds are put forward Round 1: 119 peptides, 26 chains. Longest chain 7 peptides. Score 0.251 Round 2: 135 peptides, 23 chains. Longest chain 12 peptides. Score 0.397 Round 3: 139 peptides, 23 chains. Longest chain 17 peptides. Score 0.416 Round 4: 137 peptides, 22 chains. Longest chain 14 peptides. Score 0.427 Round 5: 136 peptides, 24 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 4 Chains 22, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 5911 restraints for refining 2604 atoms. 5473 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1552 (Rfree = 0.000) for 2604 atoms. Found 14 (16 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.1456 (Rfree = 0.000) for 2601 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.1371 (Rfree = 0.000) for 2595 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.1417 (Rfree = 0.000) for 2592 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.1367 (Rfree = 0.000) for 2593 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.84 Search for helices and strands: 0 residues in 0 chains, 2655 seeds are put forward NCS extension: 0 residues added, 2655 seeds are put forward Round 1: 128 peptides, 25 chains. Longest chain 9 peptides. Score 0.320 Round 2: 142 peptides, 25 chains. Longest chain 11 peptides. Score 0.390 Round 3: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.404 Round 4: 138 peptides, 23 chains. Longest chain 13 peptides. Score 0.412 Round 5: 131 peptides, 26 chains. Longest chain 11 peptides. Score 0.314 Taking the results from Round 4 Chains 23, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 5994 restraints for refining 2620 atoms. 5557 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1551 (Rfree = 0.000) for 2620 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.1428 (Rfree = 0.000) for 2620 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.1606 (Rfree = 0.000) for 2609 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.1204 (Rfree = 0.000) for 2615 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.1125 (Rfree = 0.000) for 2604 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.79 Search for helices and strands: 0 residues in 0 chains, 2625 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2645 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 9 peptides. Score 0.256 Round 2: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.293 Round 3: 103 peptides, 19 chains. Longest chain 9 peptides. Score 0.324 Round 4: 113 peptides, 19 chains. Longest chain 12 peptides. Score 0.375 Round 5: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.352 Taking the results from Round 4 Chains 20, Residues 94, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 6072 restraints for refining 2657 atoms. 5680 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1406 (Rfree = 0.000) for 2657 atoms. Found 16 (17 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.1337 (Rfree = 0.000) for 2655 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.1367 (Rfree = 0.000) for 2660 atoms. Found 14 (17 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1285 (Rfree = 0.000) for 2660 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1515 (Rfree = 0.000) for 2664 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.72 Search for helices and strands: 0 residues in 0 chains, 2732 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2741 seeds are put forward Round 1: 92 peptides, 21 chains. Longest chain 7 peptides. Score 0.215 Round 2: 96 peptides, 20 chains. Longest chain 9 peptides. Score 0.262 Round 3: 105 peptides, 21 chains. Longest chain 11 peptides. Score 0.288 Round 4: 115 peptides, 21 chains. Longest chain 11 peptides. Score 0.341 Round 5: 94 peptides, 19 chains. Longest chain 10 peptides. Score 0.274 Taking the results from Round 4 Chains 21, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3216 reflections ( 82.48 % complete ) and 5964 restraints for refining 2604 atoms. 5609 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1478 (Rfree = 0.000) for 2604 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.1358 (Rfree = 0.000) for 2601 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.1522 (Rfree = 0.000) for 2601 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.1332 (Rfree = 0.000) for 2605 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1175 (Rfree = 0.000) for 2613 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.71 Search for helices and strands: 0 residues in 0 chains, 2674 seeds are put forward NCS extension: 0 residues added, 2674 seeds are put forward Round 1: 98 peptides, 23 chains. Longest chain 6 peptides. Score 0.202 Round 2: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.298 Round 3: 122 peptides, 24 chains. Longest chain 9 peptides. Score 0.311 Round 4: 116 peptides, 22 chains. Longest chain 13 peptides. Score 0.324 Round 5: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.298 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 94, 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 2fqp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3216 reflections ( 82.48 % complete ) and 6004 restraints for refining 2602 atoms. 5650 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1995 (Rfree = 0.000) for 2602 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1514 (Rfree = 0.000) for 2588 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1284 (Rfree = 0.000) for 2576 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1234 (Rfree = 0.000) for 2566 atoms. TimeTaking 30.27