Sun 23 Dec 22:23:08 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 2a6b-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-4.0-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/2a6b-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-4.0-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 22:23:17 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/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-4.0-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 225 and 0 Target number of residues in the AU: 225 Target solvent content: 0.6297 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 234 Adjusted target solvent content: 0.61 Input MTZ file: 2a6b-4.0-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: 90 Cell parameters: 119.176 119.176 46.302 90.000 90.000 90.000 Input sequence file: 2a6b-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.85 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: 29.794 4.000 Wilson plot Bfac: 65.98 3057 reflections ( 98.80 % complete ) and 0 restraints for refining 2089 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3303 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3310 (Rfree = 0.000) for 2089 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.08 Search for helices and strands: 0 residues in 0 chains, 2149 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 11 peptides. Score 0.309 Round 2: 119 peptides, 16 chains. Longest chain 14 peptides. Score 0.474 Round 3: 118 peptides, 15 chains. Longest chain 21 peptides. Score 0.490 Round 4: 120 peptides, 15 chains. Longest chain 16 peptides. Score 0.499 Round 5: 129 peptides, 15 chains. Longest chain 17 peptides. Score 0.538 Taking the results from Round 5 Chains 15, Residues 114, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3057 reflections ( 98.80 % complete ) and 3759 restraints for refining 1690 atoms. 3290 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2783 (Rfree = 0.000) for 1690 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 2: After refmac, R = 0.2379 (Rfree = 0.000) for 1643 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.2282 (Rfree = 0.000) for 1628 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2093 (Rfree = 0.000) for 1618 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 5: After refmac, R = 0.2079 (Rfree = 0.000) for 1598 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.06 Search for helices and strands: 0 residues in 0 chains, 1666 seeds are put forward Round 1: 111 peptides, 20 chains. Longest chain 8 peptides. Score 0.346 Round 2: 129 peptides, 17 chains. Longest chain 16 peptides. Score 0.498 Round 3: 129 peptides, 19 chains. Longest chain 13 peptides. Score 0.457 Round 4: 128 peptides, 17 chains. Longest chain 15 peptides. Score 0.494 Round 5: 129 peptides, 19 chains. Longest chain 16 peptides. Score 0.457 Taking the results from Round 2 Chains 17, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3057 reflections ( 98.80 % complete ) and 3672 restraints for refining 1623 atoms. 3241 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2550 (Rfree = 0.000) for 1623 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 7: After refmac, R = 0.2298 (Rfree = 0.000) for 1609 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.2172 (Rfree = 0.000) for 1596 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 9: After refmac, R = 0.2308 (Rfree = 0.000) for 1584 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 10: After refmac, R = 0.2198 (Rfree = 0.000) for 1567 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.05 Search for helices and strands: 0 residues in 0 chains, 1641 seeds are put forward Round 1: 115 peptides, 19 chains. Longest chain 13 peptides. Score 0.390 Round 2: 123 peptides, 19 chains. Longest chain 13 peptides. Score 0.429 Round 3: 130 peptides, 17 chains. Longest chain 18 peptides. Score 0.502 Round 4: 129 peptides, 20 chains. Longest chain 14 peptides. Score 0.436 Round 5: 130 peptides, 21 chains. Longest chain 11 peptides. Score 0.420 Taking the results from Round 3 Chains 17, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3057 reflections ( 98.80 % complete ) and 3797 restraints for refining 1691 atoms. 3362 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2661 (Rfree = 0.000) for 1691 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 12: After refmac, R = 0.2560 (Rfree = 0.000) for 1670 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 13: After refmac, R = 0.2389 (Rfree = 0.000) for 1651 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2299 (Rfree = 0.000) for 1640 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 15: After refmac, R = 0.2313 (Rfree = 0.000) for 1621 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.04 Search for helices and strands: 0 residues in 0 chains, 1702 seeds are put forward Round 1: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.372 Round 2: 133 peptides, 22 chains. Longest chain 12 peptides. Score 0.414 Round 3: 132 peptides, 19 chains. Longest chain 13 peptides. Score 0.471 Round 4: 131 peptides, 19 chains. Longest chain 13 peptides. Score 0.466 Round 5: 123 peptides, 17 chains. Longest chain 13 peptides. Score 0.471 Taking the results from Round 5 Chains 17, Residues 106, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3057 reflections ( 98.80 % complete ) and 3783 restraints for refining 1691 atoms. 3341 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2761 (Rfree = 0.000) for 1691 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 17: After refmac, R = 0.2423 (Rfree = 0.000) for 1668 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 18: After refmac, R = 0.2270 (Rfree = 0.000) for 1654 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2493 (Rfree = 0.000) for 1641 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 20: After refmac, R = 0.2126 (Rfree = 0.000) for 1631 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.05 Search for helices and strands: 0 residues in 0 chains, 1732 seeds are put forward Round 1: 112 peptides, 19 chains. Longest chain 13 peptides. Score 0.374 Round 2: 129 peptides, 16 chains. Longest chain 18 peptides. Score 0.518 Round 3: 123 peptides, 17 chains. Longest chain 17 peptides. Score 0.471 Round 4: 131 peptides, 20 chains. Longest chain 14 peptides. Score 0.446 Round 5: 130 peptides, 20 chains. Longest chain 14 peptides. Score 0.441 Taking the results from Round 2 Chains 16, Residues 113, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3057 reflections ( 98.80 % complete ) and 3614 restraints for refining 1686 atoms. 3141 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2383 (Rfree = 0.000) for 1686 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 22: After refmac, R = 0.2308 (Rfree = 0.000) for 1665 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 23: After refmac, R = 0.2414 (Rfree = 0.000) for 1645 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 24: After refmac, R = 0.2484 (Rfree = 0.000) for 1628 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 25: After refmac, R = 0.2164 (Rfree = 0.000) for 1617 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.08 Search for helices and strands: 0 residues in 0 chains, 1701 seeds are put forward Round 1: 107 peptides, 21 chains. Longest chain 9 peptides. Score 0.302 Round 2: 116 peptides, 17 chains. Longest chain 13 peptides. Score 0.438 Round 3: 116 peptides, 18 chains. Longest chain 13 peptides. Score 0.416 Round 4: 119 peptides, 16 chains. Longest chain 17 peptides. Score 0.474 Round 5: 120 peptides, 18 chains. Longest chain 20 peptides. Score 0.436 Taking the results from Round 4 Chains 16, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3057 reflections ( 98.80 % complete ) and 3793 restraints for refining 1674 atoms. 3397 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2594 (Rfree = 0.000) for 1674 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 27: After refmac, R = 0.2319 (Rfree = 0.000) for 1650 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 28: After refmac, R = 0.2425 (Rfree = 0.000) for 1631 atoms. Found 7 (7 requested) and removed 23 (3 requested) atoms. Cycle 29: After refmac, R = 0.2158 (Rfree = 0.000) for 1608 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 30: After refmac, R = 0.2095 (Rfree = 0.000) for 1593 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.05 Search for helices and strands: 0 residues in 0 chains, 1680 seeds are put forward Round 1: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.373 Round 2: 98 peptides, 15 chains. Longest chain 11 peptides. Score 0.394 Round 3: 100 peptides, 15 chains. Longest chain 14 peptides. Score 0.404 Round 4: 112 peptides, 18 chains. Longest chain 13 peptides. Score 0.397 Round 5: 107 peptides, 17 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 3 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3057 reflections ( 98.80 % complete ) and 3928 restraints for refining 1691 atoms. 3588 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2396 (Rfree = 0.000) for 1691 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 32: After refmac, R = 0.2271 (Rfree = 0.000) for 1666 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 33: After refmac, R = 0.2128 (Rfree = 0.000) for 1655 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 34: After refmac, R = 0.2043 (Rfree = 0.000) for 1642 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 35: After refmac, R = 0.2250 (Rfree = 0.000) for 1636 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.04 Search for helices and strands: 0 residues in 0 chains, 1723 seeds are put forward Round 1: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.298 Round 2: 111 peptides, 20 chains. Longest chain 15 peptides. Score 0.346 Round 3: 102 peptides, 16 chains. Longest chain 11 peptides. Score 0.391 Round 4: 109 peptides, 17 chains. Longest chain 21 peptides. Score 0.404 Round 5: 115 peptides, 18 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 5 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3057 reflections ( 98.80 % complete ) and 3942 restraints for refining 1691 atoms. 3572 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2243 (Rfree = 0.000) for 1691 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 37: After refmac, R = 0.2176 (Rfree = 0.000) for 1669 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 38: After refmac, R = 0.2309 (Rfree = 0.000) for 1655 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 39: After refmac, R = 0.2274 (Rfree = 0.000) for 1642 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 40: After refmac, R = 0.2385 (Rfree = 0.000) for 1638 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.07 Search for helices and strands: 0 residues in 0 chains, 1714 seeds are put forward Round 1: 101 peptides, 19 chains. Longest chain 11 peptides. Score 0.316 Round 2: 101 peptides, 17 chains. Longest chain 13 peptides. Score 0.363 Round 3: 103 peptides, 16 chains. Longest chain 14 peptides. Score 0.396 Round 4: 110 peptides, 15 chains. Longest chain 15 peptides. Score 0.453 Round 5: 106 peptides, 15 chains. Longest chain 15 peptides. Score 0.434 Taking the results from Round 4 Chains 15, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3057 reflections ( 98.80 % complete ) and 3986 restraints for refining 1691 atoms. 3621 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2293 (Rfree = 0.000) for 1691 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 42: After refmac, R = 0.2514 (Rfree = 0.000) for 1665 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 43: After refmac, R = 0.2353 (Rfree = 0.000) for 1644 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 44: After refmac, R = 0.2277 (Rfree = 0.000) for 1629 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 45: After refmac, R = 0.2266 (Rfree = 0.000) for 1618 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.01 Search for helices and strands: 0 residues in 0 chains, 1677 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.293 Round 2: 103 peptides, 17 chains. Longest chain 13 peptides. Score 0.373 Round 3: 103 peptides, 16 chains. Longest chain 11 peptides. Score 0.396 Round 4: 102 peptides, 17 chains. Longest chain 10 peptides. Score 0.368 Round 5: 109 peptides, 17 chains. Longest chain 20 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 92, 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 2a6b-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3057 reflections ( 98.80 % complete ) and 3602 restraints for refining 1603 atoms. 3251 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2563 (Rfree = 0.000) for 1603 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2382 (Rfree = 0.000) for 1583 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2002 (Rfree = 0.000) for 1572 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2196 (Rfree = 0.000) for 1561 atoms. TimeTaking 32.77