null Mon 24 Dec 07:58:58 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 2fzt-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fzt-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fzt-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-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/2fzt-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-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 07:59:03 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/2fzt-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-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 165 and 0 Target number of residues in the AU: 165 Target solvent content: 0.4860 Checking the provided sequence file Detected sequence length: 79 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 158 Adjusted target solvent content: 0.51 Input MTZ file: 2fzt-2.0-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: 49.630 27.430 65.380 90.000 102.600 90.000 Input sequence file: 2fzt-2.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 1264 target number of atoms Had to go as low as 0.55 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 1 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: 63.805 2.000 Wilson plot Bfac: 20.33 11159 reflections ( 99.79 % complete ) and 0 restraints for refining 1406 atoms. Observations/parameters ratio is 1.98 ------------------------------------------------------ Starting model: R = 0.3612 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3096 (Rfree = 0.000) for 1406 atoms. Found 38 (48 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.01 1.98 NCS extension: 0 residues added, 1420 seeds are put forward Round 1: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.468 Round 2: 118 peptides, 10 chains. Longest chain 35 peptides. Score 0.774 Round 3: 131 peptides, 10 chains. Longest chain 39 peptides. Score 0.822 Round 4: 135 peptides, 9 chains. Longest chain 40 peptides. Score 0.849 Round 5: 145 peptides, 5 chains. Longest chain 63 peptides. Score 0.919 Taking the results from Round 5 Chains 6, Residues 140, Estimated correctness of the model 99.3 % 2 chains (103 residues) have been docked in sequence Building loops using Loopy2018 6 chains (140 residues) following loop building 2 chains (103 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1758 restraints for refining 1392 atoms. 750 conditional restraints added. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3365 (Rfree = 0.000) for 1392 atoms. Found 37 (47 requested) and removed 26 (23 requested) atoms. Cycle 2: After refmac, R = 0.3082 (Rfree = 0.000) for 1397 atoms. Found 29 (47 requested) and removed 25 (24 requested) atoms. Cycle 3: After refmac, R = 0.2929 (Rfree = 0.000) for 1381 atoms. Found 30 (45 requested) and removed 20 (23 requested) atoms. Cycle 4: After refmac, R = 0.2821 (Rfree = 0.000) for 1387 atoms. Found 30 (44 requested) and removed 12 (23 requested) atoms. Cycle 5: After refmac, R = 0.2706 (Rfree = 0.000) for 1402 atoms. Found 20 (45 requested) and removed 9 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.95 1.92 NCS extension: 10 residues added (7 deleted due to clashes), 1424 seeds are put forward Round 1: 145 peptides, 6 chains. Longest chain 62 peptides. Score 0.908 Round 2: 149 peptides, 2 chains. Longest chain 77 peptides. Score 0.951 Round 3: 146 peptides, 5 chains. Longest chain 60 peptides. Score 0.920 Round 4: 145 peptides, 7 chains. Longest chain 49 peptides. Score 0.898 Round 5: 146 peptides, 4 chains. Longest chain 73 peptides. Score 0.930 Taking the results from Round 2 Chains 2, Residues 147, Estimated correctness of the model 99.7 % 2 chains (147 residues) have been docked in sequence Building loops using Loopy2018 2 chains (147 residues) following loop building 2 chains (147 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1460 restraints for refining 1459 atoms. 224 conditional restraints added. Observations/parameters ratio is 1.91 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2748 (Rfree = 0.000) for 1459 atoms. Found 42 (46 requested) and removed 27 (24 requested) atoms. Cycle 7: After refmac, R = 0.2581 (Rfree = 0.000) for 1473 atoms. Found 29 (46 requested) and removed 25 (25 requested) atoms. Cycle 8: After refmac, R = 0.2516 (Rfree = 0.000) for 1474 atoms. Found 24 (45 requested) and removed 12 (25 requested) atoms. Cycle 9: After refmac, R = 0.2432 (Rfree = 0.000) for 1481 atoms. Found 15 (45 requested) and removed 10 (25 requested) atoms. Cycle 10: After refmac, R = 0.2377 (Rfree = 0.000) for 1483 atoms. Found 7 (44 requested) and removed 9 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.93 1.90 NCS extension: 2 residues added (2 deleted due to clashes), 1483 seeds are put forward Round 1: 150 peptides, 4 chains. Longest chain 76 peptides. Score 0.935 Round 2: 151 peptides, 5 chains. Longest chain 61 peptides. Score 0.927 Round 3: 153 peptides, 3 chains. Longest chain 77 peptides. Score 0.947 Round 4: 146 peptides, 5 chains. Longest chain 50 peptides. Score 0.920 Round 5: 153 peptides, 4 chains. Longest chain 77 peptides. Score 0.939 Taking the results from Round 3 Chains 3, Residues 150, Estimated correctness of the model 99.7 % 3 chains (150 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1412 restraints for refining 1479 atoms. 134 conditional restraints added. Observations/parameters ratio is 1.89 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2492 (Rfree = 0.000) for 1479 atoms. Found 36 (43 requested) and removed 27 (25 requested) atoms. Cycle 12: After refmac, R = 0.2397 (Rfree = 0.000) for 1485 atoms. Found 32 (42 requested) and removed 25 (25 requested) atoms. Cycle 13: After refmac, R = 0.2282 (Rfree = 0.000) for 1492 atoms. Found 26 (42 requested) and removed 10 (25 requested) atoms. Cycle 14: After refmac, R = 0.2190 (Rfree = 0.000) for 1508 atoms. Found 35 (42 requested) and removed 9 (25 requested) atoms. Cycle 15: After refmac, R = 0.2126 (Rfree = 0.000) for 1532 atoms. Found 29 (43 requested) and removed 13 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added, 1548 seeds are put forward Round 1: 151 peptides, 4 chains. Longest chain 51 peptides. Score 0.936 Round 2: 153 peptides, 4 chains. Longest chain 61 peptides. Score 0.939 Round 3: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 4: 150 peptides, 4 chains. Longest chain 78 peptides. Score 0.935 Round 5: 153 peptides, 5 chains. Longest chain 54 peptides. Score 0.930 Taking the results from Round 3 Chains 5, Residues 150, Estimated correctness of the model 99.6 % 3 chains (144 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 B and 32 B 4 chains (152 residues) following loop building 2 chains (146 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1478 restraints for refining 1513 atoms. 231 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2288 (Rfree = 0.000) for 1513 atoms. Found 42 (42 requested) and removed 26 (25 requested) atoms. Cycle 17: After refmac, R = 0.2196 (Rfree = 0.000) for 1527 atoms. Found 40 (42 requested) and removed 16 (26 requested) atoms. Cycle 18: After refmac, R = 0.2146 (Rfree = 0.000) for 1551 atoms. Found 28 (42 requested) and removed 15 (26 requested) atoms. Cycle 19: After refmac, R = 0.2066 (Rfree = 0.000) for 1563 atoms. Found 37 (41 requested) and removed 9 (26 requested) atoms. Cycle 20: After refmac, R = 0.2048 (Rfree = 0.000) for 1590 atoms. Found 28 (42 requested) and removed 24 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.93 1.90 NCS extension: 0 residues added (8 deleted due to clashes), 1595 seeds are put forward Round 1: 152 peptides, 3 chains. Longest chain 75 peptides. Score 0.946 Round 2: 154 peptides, 3 chains. Longest chain 78 peptides. Score 0.948 Round 3: 148 peptides, 6 chains. Longest chain 48 peptides. Score 0.913 Round 4: 150 peptides, 4 chains. Longest chain 78 peptides. Score 0.935 Round 5: 152 peptides, 5 chains. Longest chain 56 peptides. Score 0.929 Taking the results from Round 2 Chains 3, Residues 151, Estimated correctness of the model 99.7 % 3 chains (151 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 B and 32 B 2 chains (153 residues) following loop building 2 chains (153 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1420 restraints for refining 1539 atoms. 134 conditional restraints added. Observations/parameters ratio is 1.81 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2245 (Rfree = 0.000) for 1539 atoms. Found 40 (40 requested) and removed 27 (26 requested) atoms. Cycle 22: After refmac, R = 0.2146 (Rfree = 0.000) for 1551 atoms. Found 36 (39 requested) and removed 21 (26 requested) atoms. Cycle 23: After refmac, R = 0.2073 (Rfree = 0.000) for 1565 atoms. Found 31 (38 requested) and removed 17 (26 requested) atoms. Cycle 24: After refmac, R = 0.2048 (Rfree = 0.000) for 1578 atoms. Found 20 (38 requested) and removed 20 (27 requested) atoms. Cycle 25: After refmac, R = 0.2013 (Rfree = 0.000) for 1576 atoms. Found 27 (37 requested) and removed 7 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.94 1.91 NCS extension: 0 residues added, 1596 seeds are put forward Round 1: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Round 2: 157 peptides, 2 chains. Longest chain 79 peptides. Score 0.959 Round 3: 155 peptides, 4 chains. Longest chain 78 peptides. Score 0.941 Round 4: 150 peptides, 9 chains. Longest chain 50 peptides. Score 0.885 Round 5: 153 peptides, 5 chains. Longest chain 63 peptides. Score 0.930 Taking the results from Round 2 Chains 3, Residues 155, Estimated correctness of the model 99.8 % 2 chains (151 residues) have been docked in sequence Building loops using Loopy2018 3 chains (155 residues) following loop building 2 chains (151 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1417 restraints for refining 1544 atoms. 131 conditional restraints added. Observations/parameters ratio is 1.81 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2206 (Rfree = 0.000) for 1544 atoms. Found 35 (35 requested) and removed 29 (26 requested) atoms. Cycle 27: After refmac, R = 0.2115 (Rfree = 0.000) for 1546 atoms. Found 35 (35 requested) and removed 15 (26 requested) atoms. Cycle 28: After refmac, R = 0.2050 (Rfree = 0.000) for 1564 atoms. Found 30 (35 requested) and removed 8 (26 requested) atoms. Cycle 29: After refmac, R = 0.2015 (Rfree = 0.000) for 1584 atoms. Found 18 (36 requested) and removed 13 (27 requested) atoms. Cycle 30: After refmac, R = 0.1963 (Rfree = 0.000) for 1589 atoms. Found 17 (35 requested) and removed 9 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.95 1.92 NCS extension: 2 residues added (1 deleted due to clashes), 1599 seeds are put forward Round 1: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Round 2: 156 peptides, 3 chains. Longest chain 79 peptides. Score 0.950 Round 3: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 4: 153 peptides, 3 chains. Longest chain 78 peptides. Score 0.947 Round 5: 148 peptides, 8 chains. Longest chain 50 peptides. Score 0.892 Taking the results from Round 2 Chains 4, Residues 153, Estimated correctness of the model 99.7 % 3 chains (149 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 A and 19 A 3 chains (155 residues) following loop building 2 chains (151 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1429 restraints for refining 1567 atoms. 143 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2143 (Rfree = 0.000) for 1567 atoms. Found 33 (33 requested) and removed 27 (26 requested) atoms. Cycle 32: After refmac, R = 0.2043 (Rfree = 0.000) for 1572 atoms. Found 20 (32 requested) and removed 13 (26 requested) atoms. Cycle 33: After refmac, R = 0.1985 (Rfree = 0.000) for 1579 atoms. Found 31 (31 requested) and removed 8 (27 requested) atoms. Cycle 34: After refmac, R = 0.1959 (Rfree = 0.000) for 1602 atoms. Found 29 (31 requested) and removed 21 (27 requested) atoms. Cycle 35: After refmac, R = 0.1966 (Rfree = 0.000) for 1610 atoms. Found 31 (31 requested) and removed 23 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.96 1.93 NCS extension: 2 residues added (1 deleted due to clashes), 1620 seeds are put forward Round 1: 154 peptides, 4 chains. Longest chain 64 peptides. Score 0.940 Round 2: 157 peptides, 2 chains. Longest chain 79 peptides. Score 0.959 Round 3: 153 peptides, 6 chains. Longest chain 61 peptides. Score 0.921 Round 4: 151 peptides, 5 chains. Longest chain 78 peptides. Score 0.927 Round 5: 150 peptides, 6 chains. Longest chain 50 peptides. Score 0.916 Taking the results from Round 2 Chains 3, Residues 155, Estimated correctness of the model 99.8 % 2 chains (151 residues) have been docked in sequence Building loops using Loopy2018 3 chains (155 residues) following loop building 2 chains (151 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1425 restraints for refining 1557 atoms. 139 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2134 (Rfree = 0.000) for 1557 atoms. Found 29 (29 requested) and removed 27 (26 requested) atoms. Cycle 37: After refmac, R = 0.2048 (Rfree = 0.000) for 1558 atoms. Found 24 (28 requested) and removed 7 (26 requested) atoms. Cycle 38: After refmac, R = 0.2016 (Rfree = 0.000) for 1574 atoms. Found 24 (28 requested) and removed 9 (26 requested) atoms. Cycle 39: After refmac, R = 0.1983 (Rfree = 0.000) for 1589 atoms. Found 25 (28 requested) and removed 14 (27 requested) atoms. Cycle 40: After refmac, R = 0.1971 (Rfree = 0.000) for 1599 atoms. Found 24 (27 requested) and removed 18 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.95 1.92 NCS extension: 2 residues added (1 deleted due to clashes), 1607 seeds are put forward Round 1: 154 peptides, 4 chains. Longest chain 64 peptides. Score 0.940 Round 2: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Round 3: 153 peptides, 5 chains. Longest chain 78 peptides. Score 0.930 Round 4: 155 peptides, 4 chains. Longest chain 78 peptides. Score 0.941 Round 5: 151 peptides, 5 chains. Longest chain 78 peptides. Score 0.927 Taking the results from Round 2 Chains 3, Residues 152, Estimated correctness of the model 99.7 % 3 chains (152 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 B and 32 B 2 chains (154 residues) following loop building 2 chains (154 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1418 restraints for refining 1559 atoms. 124 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2104 (Rfree = 0.000) for 1559 atoms. Found 26 (26 requested) and removed 27 (26 requested) atoms. Cycle 42: After refmac, R = 0.2040 (Rfree = 0.000) for 1556 atoms. Found 26 (26 requested) and removed 11 (26 requested) atoms. Cycle 43: After refmac, R = 0.2001 (Rfree = 0.000) for 1571 atoms. Found 26 (26 requested) and removed 9 (26 requested) atoms. Cycle 44: After refmac, R = 0.1965 (Rfree = 0.000) for 1588 atoms. Found 21 (27 requested) and removed 7 (27 requested) atoms. Cycle 45: After refmac, R = 0.1942 (Rfree = 0.000) for 1602 atoms. Found 18 (27 requested) and removed 13 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.94 1.91 NCS extension: 0 residues added, 1607 seeds are put forward Round 1: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 2: 156 peptides, 3 chains. Longest chain 79 peptides. Score 0.950 Round 3: 153 peptides, 5 chains. Longest chain 78 peptides. Score 0.930 Round 4: 153 peptides, 6 chains. Longest chain 54 peptides. Score 0.921 Round 5: 153 peptides, 6 chains. Longest chain 60 peptides. Score 0.921 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 153, Estimated correctness of the model 99.7 % 3 chains (149 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 29 A and 32 A 3 chains (155 residues) following loop building 2 chains (151 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 11159 reflections ( 99.79 % complete ) and 1286 restraints for refining 1283 atoms. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2741 (Rfree = 0.000) for 1283 atoms. Found 15 (21 requested) and removed 0 (21 requested) atoms. Cycle 47: After refmac, R = 0.2591 (Rfree = 0.000) for 1283 atoms. Found 6 (22 requested) and removed 0 (22 requested) atoms. Cycle 48: After refmac, R = 0.2500 (Rfree = 0.000) for 1283 atoms. Found 4 (22 requested) and removed 1 (22 requested) atoms. Cycle 49: After refmac, R = 0.2464 (Rfree = 0.000) for 1283 atoms. Found 6 (22 requested) and removed 2 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:25:01 GMT 2018 Job finished. TimeTaking 26.05 Used memory is bytes: 15236600