null Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2o2x-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2x-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-3.2-parrot-hancs ############### 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 22:23:15 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/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2x-3.2-parrot-hancs/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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6111 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 218 Adjusted target solvent content: 0.37 Input MTZ file: 2o2x-3.2-parrot-hancs.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: 36.470 66.250 41.010 90.000 108.540 90.000 Input sequence file: 2o2x-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1744 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 Loops will be built when appropriate and at the last cycle Resolution range: 38.882 3.200 Wilson plot Bfac: 56.31 3102 reflections ( 99.39 % complete ) and 0 restraints for refining 1938 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.2954 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2159 (Rfree = 0.000) for 1938 atoms. Found 8 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 3.68 Search for helices and strands: 0 residues in 0 chains, 1981 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 7 peptides. Score 0.344 Round 2: 132 peptides, 21 chains. Longest chain 15 peptides. Score 0.560 Round 3: 141 peptides, 15 chains. Longest chain 24 peptides. Score 0.748 Round 4: 156 peptides, 15 chains. Longest chain 25 peptides. Score 0.802 Round 5: 157 peptides, 14 chains. Longest chain 30 peptides. Score 0.820 Taking the results from Round 5 Chains 16, Residues 143, Estimated correctness of the model 86.3 % 3 chains (49 residues) have been docked in sequence Building loops using Loopy2018 16 chains (143 residues) following loop building 3 chains (49 residues) in sequence following loop building ------------------------------------------------------ 3102 reflections ( 99.39 % complete ) and 2899 restraints for refining 1592 atoms. 2173 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2281 (Rfree = 0.000) for 1592 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 2: After refmac, R = 0.2035 (Rfree = 0.000) for 1566 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 3: After refmac, R = 0.1955 (Rfree = 0.000) for 1557 atoms. Found 2 (13 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.1883 (Rfree = 0.000) for 1547 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2149 (Rfree = 0.000) for 1539 atoms. Found 0 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 3.64 Search for helices and strands: 0 residues in 0 chains, 1585 seeds are put forward Round 1: 121 peptides, 15 chains. Longest chain 19 peptides. Score 0.652 Round 2: 146 peptides, 16 chains. Longest chain 27 peptides. Score 0.750 Round 3: 154 peptides, 16 chains. Longest chain 23 peptides. Score 0.780 Round 4: 160 peptides, 14 chains. Longest chain 35 peptides. Score 0.828 Round 5: 153 peptides, 18 chains. Longest chain 23 peptides. Score 0.741 Taking the results from Round 4 Chains 19, Residues 146, Estimated correctness of the model 87.4 % 3 chains (42 residues) have been docked in sequence Building loops using Loopy2018 19 chains (146 residues) following loop building 3 chains (42 residues) in sequence following loop building ------------------------------------------------------ 3102 reflections ( 99.39 % complete ) and 2999 restraints for refining 1593 atoms. 2301 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2281 (Rfree = 0.000) for 1593 atoms. Found 12 (13 requested) and removed 14 (7 requested) atoms. Cycle 7: After refmac, R = 0.1952 (Rfree = 0.000) for 1583 atoms. Found 2 (12 requested) and removed 8 (7 requested) atoms. Cycle 8: After refmac, R = 0.1865 (Rfree = 0.000) for 1568 atoms. Found 3 (12 requested) and removed 7 (7 requested) atoms. Cycle 9: After refmac, R = 0.1864 (Rfree = 0.000) for 1561 atoms. Found 1 (12 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.1909 (Rfree = 0.000) for 1552 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 3.62 Search for helices and strands: 0 residues in 0 chains, 1609 seeds are put forward Round 1: 126 peptides, 17 chains. Longest chain 22 peptides. Score 0.630 Round 2: 150 peptides, 17 chains. Longest chain 26 peptides. Score 0.747 Round 3: 158 peptides, 15 chains. Longest chain 22 peptides. Score 0.808 Round 4: 151 peptides, 15 chains. Longest chain 25 peptides. Score 0.786 Round 5: 150 peptides, 14 chains. Longest chain 24 peptides. Score 0.799 Taking the results from Round 3 Chains 17, Residues 143, Estimated correctness of the model 84.6 % 4 chains (43 residues) have been docked in sequence Building loops using Loopy2018 17 chains (143 residues) following loop building 4 chains (43 residues) in sequence following loop building ------------------------------------------------------ 3102 reflections ( 99.39 % complete ) and 3122 restraints for refining 1593 atoms. 2425 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2022 (Rfree = 0.000) for 1593 atoms. Found 10 (11 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.1860 (Rfree = 0.000) for 1587 atoms. Found 4 (11 requested) and removed 7 (7 requested) atoms. Cycle 13: After refmac, R = 0.1812 (Rfree = 0.000) for 1580 atoms. Found 4 (11 requested) and removed 7 (7 requested) atoms. Cycle 14: After refmac, R = 0.1748 (Rfree = 0.000) for 1576 atoms. Found 4 (10 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.1667 (Rfree = 0.000) for 1572 atoms. Found 6 (10 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.69 Search for helices and strands: 0 residues in 0 chains, 1635 seeds are put forward Round 1: 140 peptides, 20 chains. Longest chain 17 peptides. Score 0.635 Round 2: 159 peptides, 19 chains. Longest chain 24 peptides. Score 0.746 Round 3: 149 peptides, 19 chains. Longest chain 18 peptides. Score 0.704 Round 4: 147 peptides, 18 chains. Longest chain 25 peptides. Score 0.715 Round 5: 152 peptides, 20 chains. Longest chain 26 peptides. Score 0.697 Taking the results from Round 2 Chains 19, Residues 140, Estimated correctness of the model 74.3 % 3 chains (30 residues) have been docked in sequence Building loops using Loopy2018 19 chains (140 residues) following loop building 3 chains (30 residues) in sequence following loop building ------------------------------------------------------ 3102 reflections ( 99.39 % complete ) and 3181 restraints for refining 1593 atoms. 2538 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1788 (Rfree = 0.000) for 1593 atoms. Found 10 (10 requested) and removed 13 (7 requested) atoms. Cycle 17: After refmac, R = 0.1562 (Rfree = 0.000) for 1586 atoms. Found 7 (10 requested) and removed 7 (7 requested) atoms. Cycle 18: After refmac, R = 0.1451 (Rfree = 0.000) for 1584 atoms. Found 2 (9 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.1430 (Rfree = 0.000) for 1579 atoms. Found 5 (9 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1477 (Rfree = 0.000) for 1576 atoms. Found 3 (9 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.67 Search for helices and strands: 0 residues in 0 chains, 1632 seeds are put forward Round 1: 126 peptides, 18 chains. Longest chain 20 peptides. Score 0.604 Round 2: 136 peptides, 18 chains. Longest chain 20 peptides. Score 0.661 Round 3: 130 peptides, 16 chains. Longest chain 23 peptides. Score 0.676 Round 4: 131 peptides, 16 chains. Longest chain 28 peptides. Score 0.682 Round 5: 137 peptides, 18 chains. Longest chain 25 peptides. Score 0.666 Taking the results from Round 4 Chains 16, Residues 115, Estimated correctness of the model 61.3 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3102 reflections ( 99.39 % complete ) and 3249 restraints for refining 1593 atoms. 2710 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1667 (Rfree = 0.000) for 1593 atoms. Found 8 (8 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.1491 (Rfree = 0.000) for 1589 atoms. Found 8 (8 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.1433 (Rfree = 0.000) for 1588 atoms. Found 8 (8 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.1358 (Rfree = 0.000) for 1589 atoms. Found 1 (8 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1355 (Rfree = 0.000) for 1583 atoms. Found 6 (8 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 3.67 Search for helices and strands: 0 residues in 0 chains, 1636 seeds are put forward Round 1: 102 peptides, 16 chains. Longest chain 14 peptides. Score 0.501 Round 2: 124 peptides, 17 chains. Longest chain 25 peptides. Score 0.619 Round 3: 120 peptides, 18 chains. Longest chain 17 peptides. Score 0.566 Round 4: 113 peptides, 17 chains. Longest chain 14 peptides. Score 0.549 Round 5: 112 peptides, 17 chains. Longest chain 21 peptides. Score 0.542 Taking the results from Round 2 Chains 17, Residues 107, Estimated correctness of the model 46.1 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3102 reflections ( 99.39 % complete ) and 3318 restraints for refining 1593 atoms. 2818 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1603 (Rfree = 0.000) for 1593 atoms. Found 8 (8 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.1477 (Rfree = 0.000) for 1586 atoms. Found 6 (8 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.1457 (Rfree = 0.000) for 1583 atoms. Found 3 (8 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1374 (Rfree = 0.000) for 1579 atoms. Found 2 (8 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1337 (Rfree = 0.000) for 1572 atoms. Found 6 (8 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.67 Search for helices and strands: 0 residues in 0 chains, 1626 seeds are put forward Round 1: 110 peptides, 18 chains. Longest chain 13 peptides. Score 0.497 Round 2: 127 peptides, 17 chains. Longest chain 31 peptides. Score 0.636 Round 3: 133 peptides, 15 chains. Longest chain 25 peptides. Score 0.713 Round 4: 126 peptides, 14 chains. Longest chain 31 peptides. Score 0.702 Round 5: 116 peptides, 16 chains. Longest chain 23 peptides. Score 0.597 Taking the results from Round 3 Chains 16, Residues 118, Estimated correctness of the model 67.9 % 2 chains (34 residues) have been docked in sequence Building loops using Loopy2018 16 chains (118 residues) following loop building 2 chains (34 residues) in sequence following loop building ------------------------------------------------------ 3102 reflections ( 99.39 % complete ) and 3154 restraints for refining 1593 atoms. 2571 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1687 (Rfree = 0.000) for 1593 atoms. Found 8 (8 requested) and removed 18 (7 requested) atoms. Cycle 32: After refmac, R = 0.1503 (Rfree = 0.000) for 1579 atoms. Found 6 (8 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.1448 (Rfree = 0.000) for 1576 atoms. Found 5 (8 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1454 (Rfree = 0.000) for 1574 atoms. Found 4 (8 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1477 (Rfree = 0.000) for 1571 atoms. Found 2 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 3.68 Search for helices and strands: 0 residues in 0 chains, 1609 seeds are put forward Round 1: 84 peptides, 11 chains. Longest chain 13 peptides. Score 0.531 Round 2: 94 peptides, 11 chains. Longest chain 19 peptides. Score 0.600 Round 3: 100 peptides, 11 chains. Longest chain 21 peptides. Score 0.637 Round 4: 99 peptides, 12 chains. Longest chain 15 peptides. Score 0.602 Round 5: 98 peptides, 12 chains. Longest chain 18 peptides. Score 0.596 Taking the results from Round 3 Chains 12, Residues 89, Estimated correctness of the model 50.7 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3102 reflections ( 99.39 % complete ) and 3459 restraints for refining 1581 atoms. 3056 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1618 (Rfree = 0.000) for 1581 atoms. Found 3 (7 requested) and removed 9 (7 requested) atoms. Cycle 37: After refmac, R = 0.1598 (Rfree = 0.000) for 1573 atoms. Found 4 (7 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.1569 (Rfree = 0.000) for 1569 atoms. Found 5 (7 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1531 (Rfree = 0.000) for 1566 atoms. Found 2 (7 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1507 (Rfree = 0.000) for 1561 atoms. Found 2 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.70 Search for helices and strands: 0 residues in 0 chains, 1598 seeds are put forward Round 1: 99 peptides, 15 chains. Longest chain 20 peptides. Score 0.511 Round 2: 110 peptides, 14 chains. Longest chain 24 peptides. Score 0.615 Round 3: 101 peptides, 14 chains. Longest chain 19 peptides. Score 0.556 Round 4: 106 peptides, 14 chains. Longest chain 18 peptides. Score 0.590 Round 5: 98 peptides, 15 chains. Longest chain 22 peptides. Score 0.504 Taking the results from Round 2 Chains 18, Residues 96, Estimated correctness of the model 45.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 3102 reflections ( 99.39 % complete ) and 3342 restraints for refining 1590 atoms. 2882 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1726 (Rfree = 0.000) for 1590 atoms. Found 6 (7 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.1562 (Rfree = 0.000) for 1584 atoms. Found 3 (7 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.1555 (Rfree = 0.000) for 1577 atoms. Found 2 (7 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1570 (Rfree = 0.000) for 1570 atoms. Found 5 (7 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1474 (Rfree = 0.000) for 1565 atoms. Found 6 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 3.68 Search for helices and strands: 0 residues in 0 chains, 1617 seeds are put forward Round 1: 94 peptides, 15 chains. Longest chain 20 peptides. Score 0.474 Round 2: 117 peptides, 17 chains. Longest chain 26 peptides. Score 0.575 Round 3: 111 peptides, 16 chains. Longest chain 25 peptides. Score 0.564 Round 4: 114 peptides, 16 chains. Longest chain 26 peptides. Score 0.584 Round 5: 118 peptides, 15 chains. Longest chain 25 peptides. Score 0.635 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 103, Estimated correctness of the model 50.2 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2o2x-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3102 reflections ( 99.39 % complete ) and 3476 restraints for refining 1593 atoms. 3052 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1659 (Rfree = 0.000) for 1593 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1586 (Rfree = 0.000) for 1583 atoms. Found 0 (7 requested) and removed 1 (7 requested) atoms. Cycle 48: After refmac, R = 0.1574 (Rfree = 0.000) for 1581 atoms. Found 0 (7 requested) and removed 2 (7 requested) atoms. Cycle 49: After refmac, R = 0.1414 (Rfree = 0.000) for 1579 atoms. Found 0 (7 requested) and removed 1 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:58 GMT 2018 Job finished. TimeTaking 29.88 Used memory is bytes: 18831656