null Mon 24 Dec 07:27:35 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.2-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 07:27:40 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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.2-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 252 and 0 Target number of residues in the AU: 252 Target solvent content: 0.5972 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 51.11 4635 reflections ( 83.48 % complete ) and 0 restraints for refining 3423 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3260 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2437 (Rfree = 0.000) for 3423 atoms. Found 16 (30 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.97 3.50 Search for helices and strands: 0 residues in 0 chains, 3440 seeds are put forward NCS extension: 0 residues added, 3440 seeds are put forward Round 1: 97 peptides, 18 chains. Longest chain 8 peptides. Score 0.315 Round 2: 122 peptides, 24 chains. Longest chain 8 peptides. Score 0.311 Round 3: 118 peptides, 21 chains. Longest chain 14 peptides. Score 0.356 Round 4: 118 peptides, 20 chains. Longest chain 10 peptides. Score 0.378 Round 5: 134 peptides, 24 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 4 Chains 20, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6759 restraints for refining 2834 atoms. 6387 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2176 (Rfree = 0.000) for 2834 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 2: After refmac, R = 0.2028 (Rfree = 0.000) for 2834 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 3: After refmac, R = 0.1972 (Rfree = 0.000) for 2822 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 4: After refmac, R = 0.1937 (Rfree = 0.000) for 2812 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 5: After refmac, R = 0.1901 (Rfree = 0.000) for 2802 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.97 3.50 Search for helices and strands: 0 residues in 0 chains, 2846 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2855 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 8 peptides. Score 0.278 Round 2: 149 peptides, 27 chains. Longest chain 11 peptides. Score 0.382 Round 3: 148 peptides, 24 chains. Longest chain 14 peptides. Score 0.438 Round 4: 151 peptides, 29 chains. Longest chain 12 peptides. Score 0.351 Round 5: 149 peptides, 27 chains. Longest chain 11 peptides. Score 0.382 Taking the results from Round 3 Chains 24, Residues 124, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6190 restraints for refining 2725 atoms. 5701 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2104 (Rfree = 0.000) for 2725 atoms. Found 22 (24 requested) and removed 14 (12 requested) atoms. Cycle 7: After refmac, R = 0.1967 (Rfree = 0.000) for 2721 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. Cycle 8: After refmac, R = 0.1939 (Rfree = 0.000) for 2712 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 9: After refmac, R = 0.1901 (Rfree = 0.000) for 2705 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. Cycle 10: After refmac, R = 0.1882 (Rfree = 0.000) for 2695 atoms. Found 1 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.97 3.50 Search for helices and strands: 0 residues in 0 chains, 2727 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2745 seeds are put forward Round 1: 128 peptides, 26 chains. Longest chain 8 peptides. Score 0.299 Round 2: 144 peptides, 22 chains. Longest chain 12 peptides. Score 0.459 Round 3: 146 peptides, 25 chains. Longest chain 13 peptides. Score 0.408 Round 4: 149 peptides, 24 chains. Longest chain 14 peptides. Score 0.442 Round 5: 130 peptides, 21 chains. Longest chain 14 peptides. Score 0.415 Taking the results from Round 2 Chains 22, Residues 122, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6206 restraints for refining 2686 atoms. 5724 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2042 (Rfree = 0.000) for 2686 atoms. Found 2 (24 requested) and removed 14 (12 requested) atoms. Cycle 12: After refmac, R = 0.1950 (Rfree = 0.000) for 2669 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 13: After refmac, R = 0.1908 (Rfree = 0.000) for 2658 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.1878 (Rfree = 0.000) for 2647 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.1877 (Rfree = 0.000) for 2638 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 3.52 Search for helices and strands: 0 residues in 0 chains, 2663 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2681 seeds are put forward Round 1: 115 peptides, 23 chains. Longest chain 10 peptides. Score 0.297 Round 2: 130 peptides, 22 chains. Longest chain 11 peptides. Score 0.394 Round 3: 141 peptides, 23 chains. Longest chain 11 peptides. Score 0.426 Round 4: 131 peptides, 22 chains. Longest chain 10 peptides. Score 0.399 Round 5: 139 peptides, 20 chains. Longest chain 11 peptides. Score 0.476 Taking the results from Round 5 Chains 20, Residues 119, Estimated correctness of the model 3.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6149 restraints for refining 2670 atoms. 5648 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2141 (Rfree = 0.000) for 2670 atoms. Found 17 (23 requested) and removed 17 (11 requested) atoms. Cycle 17: After refmac, R = 0.2009 (Rfree = 0.000) for 2666 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 18: After refmac, R = 0.1878 (Rfree = 0.000) for 2659 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.1776 (Rfree = 0.000) for 2648 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.1767 (Rfree = 0.000) for 2640 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.97 3.50 Search for helices and strands: 0 residues in 0 chains, 2676 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2682 seeds are put forward Round 1: 123 peptides, 25 chains. Longest chain 7 peptides. Score 0.294 Round 2: 125 peptides, 20 chains. Longest chain 11 peptides. Score 0.412 Round 3: 135 peptides, 24 chains. Longest chain 12 peptides. Score 0.377 Round 4: 149 peptides, 25 chains. Longest chain 12 peptides. Score 0.422 Round 5: 144 peptides, 24 chains. Longest chain 10 peptides. Score 0.419 Taking the results from Round 4 Chains 25, Residues 124, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6355 restraints for refining 2714 atoms. 5869 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1983 (Rfree = 0.000) for 2714 atoms. Found 12 (24 requested) and removed 13 (12 requested) atoms. Cycle 22: After refmac, R = 0.1807 (Rfree = 0.000) for 2704 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.1780 (Rfree = 0.000) for 2691 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. Cycle 24: After refmac, R = 0.1771 (Rfree = 0.000) for 2681 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.1759 (Rfree = 0.000) for 2675 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.93 3.45 Search for helices and strands: 0 residues in 0 chains, 2702 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2719 seeds are put forward Round 1: 131 peptides, 27 chains. Longest chain 9 peptides. Score 0.293 Round 2: 146 peptides, 24 chains. Longest chain 12 peptides. Score 0.429 Round 3: 139 peptides, 22 chains. Longest chain 12 peptides. Score 0.436 Round 4: 140 peptides, 20 chains. Longest chain 16 peptides. Score 0.480 Round 5: 137 peptides, 21 chains. Longest chain 18 peptides. Score 0.447 Taking the results from Round 4 Chains 20, Residues 120, Estimated correctness of the model 4.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6107 restraints for refining 2645 atoms. 5647 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1833 (Rfree = 0.000) for 2645 atoms. Found 20 (23 requested) and removed 14 (11 requested) atoms. Cycle 27: After refmac, R = 0.1670 (Rfree = 0.000) for 2648 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 28: After refmac, R = 0.1647 (Rfree = 0.000) for 2639 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.1615 (Rfree = 0.000) for 2631 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.1595 (Rfree = 0.000) for 2621 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.94 3.46 Search for helices and strands: 0 residues in 0 chains, 2672 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2688 seeds are put forward Round 1: 135 peptides, 27 chains. Longest chain 8 peptides. Score 0.313 Round 2: 150 peptides, 23 chains. Longest chain 16 peptides. Score 0.466 Round 3: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.368 Round 4: 147 peptides, 24 chains. Longest chain 17 peptides. Score 0.433 Round 5: 154 peptides, 27 chains. Longest chain 9 peptides. Score 0.406 Taking the results from Round 2 Chains 23, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6014 restraints for refining 2648 atoms. 5529 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1779 (Rfree = 0.000) for 2648 atoms. Found 14 (23 requested) and removed 11 (11 requested) atoms. Cycle 32: After refmac, R = 0.1831 (Rfree = 0.000) for 2650 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.1701 (Rfree = 0.000) for 2641 atoms. Found 6 (23 requested) and removed 12 (11 requested) atoms. Cycle 34: After refmac, R = 0.1587 (Rfree = 0.000) for 2633 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1559 (Rfree = 0.000) for 2625 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 3.53 Search for helices and strands: 0 residues in 0 chains, 2672 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 2686 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 8 peptides. Score 0.281 Round 2: 142 peptides, 25 chains. Longest chain 12 peptides. Score 0.390 Round 3: 139 peptides, 24 chains. Longest chain 14 peptides. Score 0.396 Round 4: 129 peptides, 24 chains. Longest chain 11 peptides. Score 0.347 Round 5: 146 peptides, 26 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 3 Chains 24, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6087 restraints for refining 2623 atoms. 5651 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1836 (Rfree = 0.000) for 2623 atoms. Found 17 (23 requested) and removed 11 (11 requested) atoms. Cycle 37: After refmac, R = 0.1778 (Rfree = 0.000) for 2622 atoms. Found 11 (23 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.1768 (Rfree = 0.000) for 2621 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1691 (Rfree = 0.000) for 2614 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1719 (Rfree = 0.000) for 2605 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.96 3.48 Search for helices and strands: 0 residues in 0 chains, 2634 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2652 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 11 peptides. Score 0.277 Round 2: 118 peptides, 21 chains. Longest chain 12 peptides. Score 0.356 Round 3: 120 peptides, 20 chains. Longest chain 12 peptides. Score 0.388 Round 4: 127 peptides, 22 chains. Longest chain 14 peptides. Score 0.380 Round 5: 118 peptides, 21 chains. Longest chain 9 peptides. Score 0.356 Taking the results from Round 3 Chains 20, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6154 restraints for refining 2631 atoms. 5774 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1798 (Rfree = 0.000) for 2631 atoms. Found 13 (23 requested) and removed 11 (11 requested) atoms. Cycle 42: After refmac, R = 0.1803 (Rfree = 0.000) for 2632 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.1703 (Rfree = 0.000) for 2625 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.1703 (Rfree = 0.000) for 2614 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1686 (Rfree = 0.000) for 2607 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.97 3.50 Search for helices and strands: 0 residues in 0 chains, 2636 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2654 seeds are put forward Round 1: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.300 Round 2: 109 peptides, 20 chains. Longest chain 9 peptides. Score 0.332 Round 3: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.333 Round 4: 92 peptides, 16 chains. Longest chain 12 peptides. Score 0.335 Round 5: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.321 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 76, 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. 4635 reflections ( 83.48 % complete ) and 6362 restraints for refining 2600 atoms. 6074 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1712 (Rfree = 0.000) for 2600 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1521 (Rfree = 0.000) for 2589 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1512 (Rfree = 0.000) for 2578 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1362 (Rfree = 0.000) for 2567 atoms. Found 0 (23 requested) and removed 3 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:59:29 GMT 2018 Job finished. TimeTaking 31.89 Used memory is bytes: 13141208