Sun 23 Dec 22:23:10 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 2o2g-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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/2o2g-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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 22:23:20 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/2o2g-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-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 146 and 0 Target number of residues in the AU: 146 Target solvent content: 0.6113 Checking the provided sequence file Detected sequence length: 223 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 223 Adjusted target solvent content: 0.41 Input MTZ file: 2o2g-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: 19 Cell parameters: 47.887 62.444 67.988 90.000 90.000 90.000 Input sequence file: 2o2g-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1784 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 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: 45.990 3.200 Wilson plot Bfac: 56.91 3414 reflections ( 93.79 % complete ) and 0 restraints for refining 1987 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3723 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3252 (Rfree = 0.000) for 1987 atoms. Found 11 (17 requested) and removed 33 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 1997 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 10 peptides. Score 0.271 Round 2: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.329 Round 3: 87 peptides, 16 chains. Longest chain 11 peptides. Score 0.370 Round 4: 90 peptides, 14 chains. Longest chain 14 peptides. Score 0.460 Round 5: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 4 Chains 14, Residues 76, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3414 reflections ( 93.79 % complete ) and 3795 restraints for refining 1629 atoms. 3474 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2889 (Rfree = 0.000) for 1629 atoms. Found 13 (14 requested) and removed 14 (7 requested) atoms. Cycle 2: After refmac, R = 0.2816 (Rfree = 0.000) for 1615 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.2456 (Rfree = 0.000) for 1609 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2346 (Rfree = 0.000) for 1601 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2932 (Rfree = 0.000) for 1591 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 1652 seeds are put forward Round 1: 100 peptides, 18 chains. Longest chain 11 peptides. Score 0.405 Round 2: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.467 Round 3: 107 peptides, 17 chains. Longest chain 13 peptides. Score 0.488 Round 4: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.467 Round 5: 104 peptides, 15 chains. Longest chain 12 peptides. Score 0.527 Taking the results from Round 5 Chains 15, Residues 89, Estimated correctness of the model 19.9 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3414 reflections ( 93.79 % complete ) and 3711 restraints for refining 1628 atoms. 3310 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2894 (Rfree = 0.000) for 1628 atoms. Found 11 (14 requested) and removed 15 (7 requested) atoms. Cycle 7: After refmac, R = 0.2869 (Rfree = 0.000) for 1619 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 8: After refmac, R = 0.2701 (Rfree = 0.000) for 1619 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2432 (Rfree = 0.000) for 1611 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 10: After refmac, R = 0.2300 (Rfree = 0.000) for 1606 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 1642 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 8 peptides. Score 0.324 Round 2: 115 peptides, 17 chains. Longest chain 17 peptides. Score 0.541 Round 3: 109 peptides, 18 chains. Longest chain 18 peptides. Score 0.472 Round 4: 100 peptides, 15 chains. Longest chain 17 peptides. Score 0.500 Round 5: 104 peptides, 16 chains. Longest chain 19 peptides. Score 0.497 Taking the results from Round 2 Chains 18, Residues 98, Estimated correctness of the model 24.2 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3414 reflections ( 93.79 % complete ) and 3546 restraints for refining 1629 atoms. 3125 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2497 (Rfree = 0.000) for 1629 atoms. Found 7 (14 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.2534 (Rfree = 0.000) for 1621 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2812 (Rfree = 0.000) for 1615 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Cycle 14: After refmac, R = 0.2487 (Rfree = 0.000) for 1614 atoms. Found 1 (14 requested) and removed 11 (7 requested) atoms. Cycle 15: After refmac, R = 0.2488 (Rfree = 0.000) for 1603 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 1649 seeds are put forward Round 1: 89 peptides, 19 chains. Longest chain 9 peptides. Score 0.282 Round 2: 105 peptides, 16 chains. Longest chain 14 peptides. Score 0.504 Round 3: 103 peptides, 16 chains. Longest chain 16 peptides. Score 0.490 Round 4: 105 peptides, 15 chains. Longest chain 16 peptides. Score 0.534 Round 5: 95 peptides, 15 chains. Longest chain 14 peptides. Score 0.464 Taking the results from Round 4 Chains 15, Residues 90, Estimated correctness of the model 22.1 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3414 reflections ( 93.79 % complete ) and 3787 restraints for refining 1629 atoms. 3416 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2845 (Rfree = 0.000) for 1629 atoms. Found 10 (14 requested) and removed 13 (7 requested) atoms. Cycle 17: After refmac, R = 0.2375 (Rfree = 0.000) for 1619 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 18: After refmac, R = 0.2174 (Rfree = 0.000) for 1605 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.2166 (Rfree = 0.000) for 1600 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.2007 (Rfree = 0.000) for 1591 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 1633 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.324 Round 2: 82 peptides, 12 chains. Longest chain 14 peptides. Score 0.466 Round 3: 90 peptides, 16 chains. Longest chain 15 peptides. Score 0.394 Round 4: 93 peptides, 15 chains. Longest chain 15 peptides. Score 0.450 Round 5: 81 peptides, 13 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 2 Chains 12, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3414 reflections ( 93.79 % complete ) and 3814 restraints for refining 1598 atoms. 3546 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2289 (Rfree = 0.000) for 1598 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Cycle 22: After refmac, R = 0.2559 (Rfree = 0.000) for 1595 atoms. Found 9 (14 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.2213 (Rfree = 0.000) for 1594 atoms. Found 9 (14 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.1845 (Rfree = 0.000) for 1582 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2318 (Rfree = 0.000) for 1577 atoms. Found 6 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 1617 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 13 peptides. Score 0.315 Round 2: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.396 Round 3: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.430 Round 4: 89 peptides, 14 chains. Longest chain 12 peptides. Score 0.452 Round 5: 85 peptides, 13 chains. Longest chain 16 peptides. Score 0.455 Taking the results from Round 5 Chains 13, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3414 reflections ( 93.79 % complete ) and 3603 restraints for refining 1587 atoms. 3328 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2346 (Rfree = 0.000) for 1587 atoms. Found 8 (14 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.2269 (Rfree = 0.000) for 1581 atoms. Found 9 (14 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.1840 (Rfree = 0.000) for 1577 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. Cycle 29: After refmac, R = 0.1865 (Rfree = 0.000) for 1572 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 30: After refmac, R = 0.1979 (Rfree = 0.000) for 1566 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.54 Search for helices and strands: 0 residues in 0 chains, 1598 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 6 peptides. Score 0.249 Round 2: 75 peptides, 13 chains. Longest chain 16 peptides. Score 0.377 Round 3: 77 peptides, 13 chains. Longest chain 12 peptides. Score 0.393 Round 4: 71 peptides, 10 chains. Longest chain 18 peptides. Score 0.451 Round 5: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.417 Taking the results from Round 4 Chains 10, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3414 reflections ( 93.79 % complete ) and 3832 restraints for refining 1608 atoms. 3598 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2034 (Rfree = 0.000) for 1608 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 32: After refmac, R = 0.2120 (Rfree = 0.000) for 1607 atoms. Found 11 (14 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.2157 (Rfree = 0.000) for 1609 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.2061 (Rfree = 0.000) for 1608 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.2043 (Rfree = 0.000) for 1607 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.53 Search for helices and strands: 0 residues in 0 chains, 1653 seeds are put forward Round 1: 68 peptides, 13 chains. Longest chain 11 peptides. Score 0.318 Round 2: 72 peptides, 13 chains. Longest chain 10 peptides. Score 0.352 Round 3: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.385 Round 4: 68 peptides, 12 chains. Longest chain 11 peptides. Score 0.355 Round 5: 80 peptides, 11 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 5 Chains 12, Residues 69, Estimated correctness of the model 6.1 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3414 reflections ( 93.79 % complete ) and 3743 restraints for refining 1629 atoms. 3431 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2064 (Rfree = 0.000) for 1629 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 37: After refmac, R = 0.1923 (Rfree = 0.000) for 1626 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.1991 (Rfree = 0.000) for 1625 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1948 (Rfree = 0.000) for 1621 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1842 (Rfree = 0.000) for 1617 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 1648 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 16 peptides. Score 0.326 Round 2: 77 peptides, 11 chains. Longest chain 17 peptides. Score 0.462 Round 3: 77 peptides, 11 chains. Longest chain 16 peptides. Score 0.462 Round 4: 85 peptides, 13 chains. Longest chain 18 peptides. Score 0.455 Round 5: 79 peptides, 12 chains. Longest chain 17 peptides. Score 0.443 Taking the results from Round 3 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3414 reflections ( 93.79 % complete ) and 3858 restraints for refining 1621 atoms. 3605 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2171 (Rfree = 0.000) for 1621 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.1980 (Rfree = 0.000) for 1627 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.2738 (Rfree = 0.000) for 1622 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.2141 (Rfree = 0.000) for 1628 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.2297 (Rfree = 0.000) for 1629 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 1687 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 10 peptides. Score 0.270 Round 2: 59 peptides, 9 chains. Longest chain 13 peptides. Score 0.391 Round 3: 58 peptides, 9 chains. Longest chain 10 peptides. Score 0.382 Round 4: 61 peptides, 9 chains. Longest chain 12 peptides. Score 0.407 Round 5: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.311 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 52, 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 2o2g-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3414 reflections ( 93.79 % complete ) and 3988 restraints for refining 1625 atoms. 3789 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2262 (Rfree = 0.000) for 1625 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2055 (Rfree = 0.000) for 1615 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1968 (Rfree = 0.000) for 1604 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1838 (Rfree = 0.000) for 1595 atoms. TimeTaking 28.82