Sun 23 Dec 23:44:13 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 2od4-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-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/2od4-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-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 23:44:17 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/2od4-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-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 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.6198 Checking the provided sequence file Detected sequence length: 101 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 202 Adjusted target solvent content: 0.48 Input MTZ file: 2od4-3.2-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: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1616 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 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: 28.889 3.200 Wilson plot Bfac: 61.23 3433 reflections ( 98.54 % complete ) and 0 restraints for refining 1783 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3165 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2406 (Rfree = 0.000) for 1783 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward NCS extension: 0 residues added, 1826 seeds are put forward Round 1: 94 peptides, 15 chains. Longest chain 12 peptides. Score 0.448 Round 2: 109 peptides, 15 chains. Longest chain 12 peptides. Score 0.548 Round 3: 126 peptides, 17 chains. Longest chain 14 peptides. Score 0.596 Round 4: 135 peptides, 16 chains. Longest chain 15 peptides. Score 0.666 Round 5: 142 peptides, 18 chains. Longest chain 13 peptides. Score 0.656 Taking the results from Round 4 Chains 16, Residues 119, Estimated correctness of the model 57.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3143 restraints for refining 1476 atoms. 2683 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2308 (Rfree = 0.000) for 1476 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 2: After refmac, R = 0.2105 (Rfree = 0.000) for 1464 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 3: After refmac, R = 0.2016 (Rfree = 0.000) for 1454 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.1954 (Rfree = 0.000) for 1451 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.1930 (Rfree = 0.000) for 1444 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 1509 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1528 seeds are put forward Round 1: 124 peptides, 18 chains. Longest chain 14 peptides. Score 0.559 Round 2: 127 peptides, 16 chains. Longest chain 17 peptides. Score 0.626 Round 3: 130 peptides, 13 chains. Longest chain 20 peptides. Score 0.706 Round 4: 133 peptides, 15 chains. Longest chain 15 peptides. Score 0.678 Round 5: 131 peptides, 16 chains. Longest chain 15 peptides. Score 0.646 Taking the results from Round 3 Chains 13, Residues 117, Estimated correctness of the model 66.4 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3122 restraints for refining 1476 atoms. 2620 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2317 (Rfree = 0.000) for 1476 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 7: After refmac, R = 0.2140 (Rfree = 0.000) for 1471 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2081 (Rfree = 0.000) for 1461 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2021 (Rfree = 0.000) for 1455 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2012 (Rfree = 0.000) for 1450 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 1486 seeds are put forward NCS extension: 0 residues added, 1486 seeds are put forward Round 1: 129 peptides, 15 chains. Longest chain 18 peptides. Score 0.659 Round 2: 136 peptides, 15 chains. Longest chain 19 peptides. Score 0.692 Round 3: 142 peptides, 15 chains. Longest chain 20 peptides. Score 0.717 Round 4: 137 peptides, 14 chains. Longest chain 20 peptides. Score 0.716 Round 5: 134 peptides, 15 chains. Longest chain 20 peptides. Score 0.683 Taking the results from Round 3 Chains 15, Residues 127, Estimated correctness of the model 68.7 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3053 restraints for refining 1476 atoms. 2501 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2292 (Rfree = 0.000) for 1476 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 12: After refmac, R = 0.2364 (Rfree = 0.000) for 1477 atoms. Found 9 (11 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.2438 (Rfree = 0.000) for 1475 atoms. Found 11 (11 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.1907 (Rfree = 0.000) for 1473 atoms. Found 1 (11 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1931 (Rfree = 0.000) for 1466 atoms. Found 3 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 1522 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 1552 seeds are put forward Round 1: 140 peptides, 16 chains. Longest chain 20 peptides. Score 0.689 Round 2: 149 peptides, 15 chains. Longest chain 21 peptides. Score 0.745 Round 3: 147 peptides, 15 chains. Longest chain 21 peptides. Score 0.737 Round 4: 145 peptides, 17 chains. Longest chain 21 peptides. Score 0.691 Round 5: 143 peptides, 14 chains. Longest chain 22 peptides. Score 0.740 Taking the results from Round 2 Chains 16, Residues 134, Estimated correctness of the model 74.1 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 2953 restraints for refining 1476 atoms. 2374 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2019 (Rfree = 0.000) for 1476 atoms. Found 4 (10 requested) and removed 7 (6 requested) atoms. Cycle 17: After refmac, R = 0.1883 (Rfree = 0.000) for 1470 atoms. Found 2 (10 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.1840 (Rfree = 0.000) for 1464 atoms. Found 3 (10 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.1782 (Rfree = 0.000) for 1461 atoms. Found 1 (10 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.1745 (Rfree = 0.000) for 1455 atoms. Found 0 (9 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 1498 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 1526 seeds are put forward Round 1: 132 peptides, 15 chains. Longest chain 19 peptides. Score 0.673 Round 2: 141 peptides, 16 chains. Longest chain 21 peptides. Score 0.693 Round 3: 141 peptides, 13 chains. Longest chain 27 peptides. Score 0.751 Round 4: 146 peptides, 15 chains. Longest chain 21 peptides. Score 0.733 Round 5: 129 peptides, 16 chains. Longest chain 21 peptides. Score 0.636 Taking the results from Round 3 Chains 13, Residues 128, Estimated correctness of the model 75.2 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3012 restraints for refining 1476 atoms. 2450 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2182 (Rfree = 0.000) for 1476 atoms. Found 8 (9 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2014 (Rfree = 0.000) for 1474 atoms. Found 6 (9 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.1849 (Rfree = 0.000) for 1470 atoms. Found 2 (9 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1833 (Rfree = 0.000) for 1464 atoms. Found 3 (8 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1797 (Rfree = 0.000) for 1461 atoms. Found 3 (8 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 1511 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1535 seeds are put forward Round 1: 130 peptides, 16 chains. Longest chain 23 peptides. Score 0.641 Round 2: 138 peptides, 15 chains. Longest chain 27 peptides. Score 0.701 Round 3: 143 peptides, 15 chains. Longest chain 27 peptides. Score 0.722 Round 4: 144 peptides, 16 chains. Longest chain 28 peptides. Score 0.706 Round 5: 144 peptides, 13 chains. Longest chain 28 peptides. Score 0.761 Taking the results from Round 5 Chains 15, Residues 131, Estimated correctness of the model 77.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3054 restraints for refining 1476 atoms. 2499 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2088 (Rfree = 0.000) for 1476 atoms. Found 8 (8 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.1888 (Rfree = 0.000) for 1471 atoms. Found 6 (8 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.1884 (Rfree = 0.000) for 1471 atoms. Found 2 (7 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.1957 (Rfree = 0.000) for 1465 atoms. Found 5 (7 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.1752 (Rfree = 0.000) for 1464 atoms. Found 3 (7 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 1506 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1527 seeds are put forward Round 1: 123 peptides, 14 chains. Longest chain 31 peptides. Score 0.652 Round 2: 131 peptides, 14 chains. Longest chain 27 peptides. Score 0.690 Round 3: 129 peptides, 14 chains. Longest chain 21 peptides. Score 0.681 Round 4: 128 peptides, 15 chains. Longest chain 21 peptides. Score 0.654 Round 5: 123 peptides, 14 chains. Longest chain 24 peptides. Score 0.652 Taking the results from Round 2 Chains 14, Residues 117, Estimated correctness of the model 63.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3270 restraints for refining 1476 atoms. 2816 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1880 (Rfree = 0.000) for 1476 atoms. Found 3 (6 requested) and removed 7 (6 requested) atoms. Cycle 32: After refmac, R = 0.1807 (Rfree = 0.000) for 1469 atoms. Found 4 (6 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.1774 (Rfree = 0.000) for 1467 atoms. Found 1 (6 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1806 (Rfree = 0.000) for 1462 atoms. Found 0 (6 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1748 (Rfree = 0.000) for 1456 atoms. Found 0 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 1490 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 1528 seeds are put forward Round 1: 95 peptides, 13 chains. Longest chain 12 peptides. Score 0.516 Round 2: 119 peptides, 15 chains. Longest chain 32 peptides. Score 0.607 Round 3: 123 peptides, 14 chains. Longest chain 24 peptides. Score 0.652 Round 4: 129 peptides, 15 chains. Longest chain 24 peptides. Score 0.659 Round 5: 124 peptides, 16 chains. Longest chain 18 peptides. Score 0.610 Taking the results from Round 4 Chains 15, Residues 114, Estimated correctness of the model 56.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3162 restraints for refining 1476 atoms. 2671 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2045 (Rfree = 0.000) for 1476 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.1925 (Rfree = 0.000) for 1470 atoms. Found 1 (6 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.1900 (Rfree = 0.000) for 1465 atoms. Found 2 (6 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.1874 (Rfree = 0.000) for 1460 atoms. Found 2 (6 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1876 (Rfree = 0.000) for 1455 atoms. Found 3 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 1515 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 1553 seeds are put forward Round 1: 109 peptides, 16 chains. Longest chain 19 peptides. Score 0.520 Round 2: 113 peptides, 13 chains. Longest chain 31 peptides. Score 0.624 Round 3: 117 peptides, 14 chains. Longest chain 35 peptides. Score 0.621 Round 4: 118 peptides, 14 chains. Longest chain 29 peptides. Score 0.626 Round 5: 121 peptides, 16 chains. Longest chain 18 peptides. Score 0.593 Taking the results from Round 4 Chains 14, Residues 104, Estimated correctness of the model 47.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3312 restraints for refining 1476 atoms. 2910 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2060 (Rfree = 0.000) for 1476 atoms. Found 6 (6 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.1949 (Rfree = 0.000) for 1476 atoms. Found 3 (6 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.1909 (Rfree = 0.000) for 1473 atoms. Found 2 (6 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1908 (Rfree = 0.000) for 1469 atoms. Found 1 (6 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1885 (Rfree = 0.000) for 1464 atoms. Found 3 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 1506 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 1542 seeds are put forward Round 1: 101 peptides, 14 chains. Longest chain 20 peptides. Score 0.526 Round 2: 121 peptides, 15 chains. Longest chain 20 peptides. Score 0.618 Round 3: 132 peptides, 15 chains. Longest chain 35 peptides. Score 0.673 Round 4: 123 peptides, 14 chains. Longest chain 23 peptides. Score 0.652 Round 5: 122 peptides, 14 chains. Longest chain 20 peptides. Score 0.647 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 117, Estimated correctness of the model 59.2 % 1 chains (28 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 2od4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3433 reflections ( 98.54 % complete ) and 2900 restraints for refining 1476 atoms. 2322 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2213 (Rfree = 0.000) for 1476 atoms. Found 0 (6 requested) and removed 1 (6 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 1472 atoms. Found 0 (6 requested) and removed 1 (6 requested) atoms. Cycle 48: After refmac, R = 0.2053 (Rfree = 0.000) for 1470 atoms. Found 0 (6 requested) and removed 0 (6 requested) atoms. Cycle 49: After refmac, R = 0.2028 (Rfree = 0.000) for 1470 atoms. TimeTaking 22.23