Sun 23 Dec 22:22:42 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 1vme-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vme-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vme-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.4-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/1vme-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.4-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 22:22:56 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/1vme-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.4-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 623 and 0 Target number of residues in the AU: 623 Target solvent content: 0.6451 Checking the provided sequence file Detected sequence length: 410 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 820 Adjusted target solvent content: 0.53 Input MTZ file: 1vme-3.4-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: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 6560 target number of atoms Had to go as low as 0.70 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: 48.998 3.400 Wilson plot Bfac: 74.80 12971 reflections ( 99.85 % complete ) and 0 restraints for refining 7287 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3130 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2757 (Rfree = 0.000) for 7287 atoms. Found 55 (55 requested) and removed 78 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.22 Search for helices and strands: 0 residues in 0 chains, 7402 seeds are put forward NCS extension: 0 residues added, 7402 seeds are put forward Round 1: 455 peptides, 72 chains. Longest chain 14 peptides. Score 0.468 Round 2: 520 peptides, 67 chains. Longest chain 27 peptides. Score 0.591 Round 3: 550 peptides, 67 chains. Longest chain 20 peptides. Score 0.628 Round 4: 560 peptides, 58 chains. Longest chain 30 peptides. Score 0.685 Round 5: 568 peptides, 59 chains. Longest chain 28 peptides. Score 0.688 Taking the results from Round 5 Chains 64, Residues 509, Estimated correctness of the model 54.7 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12449 restraints for refining 5964 atoms. 10288 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2512 (Rfree = 0.000) for 5964 atoms. Found 34 (45 requested) and removed 40 (22 requested) atoms. Cycle 2: After refmac, R = 0.2375 (Rfree = 0.000) for 5869 atoms. Found 11 (44 requested) and removed 46 (22 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2267 (Rfree = 0.000) for 5799 atoms. Found 11 (44 requested) and removed 31 (22 requested) atoms. Cycle 4: After refmac, R = 0.2235 (Rfree = 0.000) for 5755 atoms. Found 16 (43 requested) and removed 26 (21 requested) atoms. Cycle 5: After refmac, R = 0.2132 (Rfree = 0.000) for 5730 atoms. Found 9 (43 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 5920 seeds are put forward NCS extension: 38 residues added (7 deleted due to clashes), 5958 seeds are put forward Round 1: 509 peptides, 60 chains. Longest chain 32 peptides. Score 0.617 Round 2: 568 peptides, 55 chains. Longest chain 35 peptides. Score 0.707 Round 3: 584 peptides, 55 chains. Longest chain 38 peptides. Score 0.722 Round 4: 577 peptides, 51 chains. Longest chain 38 peptides. Score 0.733 Round 5: 554 peptides, 58 chains. Longest chain 32 peptides. Score 0.678 Taking the results from Round 4 Chains 63, Residues 526, Estimated correctness of the model 66.0 % 10 chains (112 residues) have been docked in sequence Building loops using Loopy2018 63 chains (526 residues) following loop building 10 chains (112 residues) in sequence following loop building ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 11643 restraints for refining 5964 atoms. 9167 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2520 (Rfree = 0.000) for 5964 atoms. Found 40 (45 requested) and removed 56 (22 requested) atoms. Cycle 7: After refmac, R = 0.2291 (Rfree = 0.000) for 5919 atoms. Found 16 (43 requested) and removed 31 (22 requested) atoms. Cycle 8: After refmac, R = 0.2210 (Rfree = 0.000) for 5883 atoms. Found 13 (42 requested) and removed 26 (22 requested) atoms. Cycle 9: After refmac, R = 0.2181 (Rfree = 0.000) for 5855 atoms. Found 8 (41 requested) and removed 23 (22 requested) atoms. Cycle 10: After refmac, R = 0.2146 (Rfree = 0.000) for 5827 atoms. Found 10 (40 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 5986 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6003 seeds are put forward Round 1: 519 peptides, 64 chains. Longest chain 25 peptides. Score 0.607 Round 2: 539 peptides, 53 chains. Longest chain 24 peptides. Score 0.687 Round 3: 564 peptides, 55 chains. Longest chain 31 peptides. Score 0.703 Round 4: 554 peptides, 53 chains. Longest chain 31 peptides. Score 0.702 Round 5: 545 peptides, 58 chains. Longest chain 31 peptides. Score 0.669 Taking the results from Round 3 Chains 60, Residues 509, Estimated correctness of the model 58.6 % 7 chains (101 residues) have been docked in sequence Building loops using Loopy2018 60 chains (509 residues) following loop building 7 chains (101 residues) in sequence following loop building ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 11771 restraints for refining 5964 atoms. 9385 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2422 (Rfree = 0.000) for 5964 atoms. Found 32 (40 requested) and removed 51 (22 requested) atoms. Cycle 12: After refmac, R = 0.2308 (Rfree = 0.000) for 5914 atoms. Found 15 (39 requested) and removed 32 (22 requested) atoms. Cycle 13: After refmac, R = 0.2301 (Rfree = 0.000) for 5877 atoms. Found 16 (38 requested) and removed 26 (22 requested) atoms. Cycle 14: After refmac, R = 0.2271 (Rfree = 0.000) for 5857 atoms. Found 11 (37 requested) and removed 27 (22 requested) atoms. Cycle 15: After refmac, R = 0.2205 (Rfree = 0.000) for 5831 atoms. Found 10 (36 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 6008 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 6035 seeds are put forward Round 1: 474 peptides, 67 chains. Longest chain 17 peptides. Score 0.529 Round 2: 520 peptides, 58 chains. Longest chain 22 peptides. Score 0.641 Round 3: 551 peptides, 59 chains. Longest chain 27 peptides. Score 0.670 Round 4: 550 peptides, 62 chains. Longest chain 29 peptides. Score 0.654 Round 5: 550 peptides, 57 chains. Longest chain 27 peptides. Score 0.679 Taking the results from Round 5 Chains 61, Residues 493, Estimated correctness of the model 52.3 % 7 chains (94 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12025 restraints for refining 5964 atoms. 9736 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2350 (Rfree = 0.000) for 5964 atoms. Found 35 (36 requested) and removed 47 (22 requested) atoms. Cycle 17: After refmac, R = 0.2216 (Rfree = 0.000) for 5934 atoms. Found 19 (35 requested) and removed 29 (22 requested) atoms. Cycle 18: After refmac, R = 0.2190 (Rfree = 0.000) for 5911 atoms. Found 9 (35 requested) and removed 26 (22 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2152 (Rfree = 0.000) for 5887 atoms. Found 19 (35 requested) and removed 23 (22 requested) atoms. Cycle 20: After refmac, R = 0.2137 (Rfree = 0.000) for 5880 atoms. Found 15 (35 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6055 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 6079 seeds are put forward Round 1: 483 peptides, 67 chains. Longest chain 20 peptides. Score 0.542 Round 2: 526 peptides, 61 chains. Longest chain 24 peptides. Score 0.632 Round 3: 531 peptides, 60 chains. Longest chain 25 peptides. Score 0.643 Round 4: 542 peptides, 60 chains. Longest chain 22 peptides. Score 0.655 Round 5: 556 peptides, 63 chains. Longest chain 30 peptides. Score 0.656 Taking the results from Round 5 Chains 66, Residues 493, Estimated correctness of the model 45.9 % 5 chains (77 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12172 restraints for refining 5965 atoms. 9953 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2380 (Rfree = 0.000) for 5965 atoms. Found 36 (36 requested) and removed 40 (22 requested) atoms. Cycle 22: After refmac, R = 0.2223 (Rfree = 0.000) for 5947 atoms. Found 11 (36 requested) and removed 30 (22 requested) atoms. Cycle 23: After refmac, R = 0.2196 (Rfree = 0.000) for 5913 atoms. Found 13 (35 requested) and removed 28 (22 requested) atoms. Cycle 24: After refmac, R = 0.2186 (Rfree = 0.000) for 5890 atoms. Found 13 (35 requested) and removed 23 (22 requested) atoms. Cycle 25: After refmac, R = 0.2134 (Rfree = 0.000) for 5877 atoms. Found 10 (35 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 6036 seeds are put forward NCS extension: 34 residues added (7 deleted due to clashes), 6070 seeds are put forward Round 1: 476 peptides, 74 chains. Longest chain 15 peptides. Score 0.487 Round 2: 528 peptides, 70 chains. Longest chain 23 peptides. Score 0.584 Round 3: 528 peptides, 66 chains. Longest chain 21 peptides. Score 0.607 Round 4: 513 peptides, 61 chains. Longest chain 22 peptides. Score 0.616 Round 5: 501 peptides, 60 chains. Longest chain 20 peptides. Score 0.607 Taking the results from Round 4 Chains 63, Residues 452, Estimated correctness of the model 33.8 % 6 chains (61 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12578 restraints for refining 5963 atoms. 10599 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2412 (Rfree = 0.000) for 5963 atoms. Found 33 (36 requested) and removed 45 (22 requested) atoms. Cycle 27: After refmac, R = 0.2251 (Rfree = 0.000) for 5924 atoms. Found 19 (35 requested) and removed 28 (22 requested) atoms. Cycle 28: After refmac, R = 0.2181 (Rfree = 0.000) for 5905 atoms. Found 9 (35 requested) and removed 24 (22 requested) atoms. Cycle 29: After refmac, R = 0.2129 (Rfree = 0.000) for 5882 atoms. Found 11 (35 requested) and removed 24 (22 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2120 (Rfree = 0.000) for 5860 atoms. Found 12 (35 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6021 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6045 seeds are put forward Round 1: 424 peptides, 77 chains. Longest chain 15 peptides. Score 0.383 Round 2: 479 peptides, 71 chains. Longest chain 19 peptides. Score 0.511 Round 3: 466 peptides, 64 chains. Longest chain 22 peptides. Score 0.537 Round 4: 487 peptides, 63 chains. Longest chain 22 peptides. Score 0.572 Round 5: 459 peptides, 64 chains. Longest chain 17 peptides. Score 0.527 Taking the results from Round 4 Chains 63, Residues 424, Estimated correctness of the model 19.3 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 13153 restraints for refining 5965 atoms. 11451 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2280 (Rfree = 0.000) for 5965 atoms. Found 29 (36 requested) and removed 26 (22 requested) atoms. Cycle 32: After refmac, R = 0.2151 (Rfree = 0.000) for 5942 atoms. Found 22 (36 requested) and removed 26 (22 requested) atoms. Cycle 33: After refmac, R = 0.2103 (Rfree = 0.000) for 5929 atoms. Found 23 (35 requested) and removed 24 (22 requested) atoms. Cycle 34: After refmac, R = 0.2031 (Rfree = 0.000) for 5918 atoms. Found 15 (35 requested) and removed 24 (22 requested) atoms. Cycle 35: After refmac, R = 0.2020 (Rfree = 0.000) for 5903 atoms. Found 14 (35 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6023 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 6042 seeds are put forward Round 1: 413 peptides, 69 chains. Longest chain 15 peptides. Score 0.422 Round 2: 428 peptides, 61 chains. Longest chain 20 peptides. Score 0.501 Round 3: 422 peptides, 56 chains. Longest chain 25 peptides. Score 0.525 Round 4: 432 peptides, 55 chains. Longest chain 20 peptides. Score 0.546 Round 5: 430 peptides, 53 chains. Longest chain 30 peptides. Score 0.556 Taking the results from Round 5 Chains 56, Residues 377, Estimated correctness of the model 13.7 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 13390 restraints for refining 5965 atoms. 11794 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2246 (Rfree = 0.000) for 5965 atoms. Found 33 (36 requested) and removed 32 (22 requested) atoms. Cycle 37: After refmac, R = 0.2112 (Rfree = 0.000) for 5948 atoms. Found 12 (36 requested) and removed 28 (22 requested) atoms. Cycle 38: After refmac, R = 0.2212 (Rfree = 0.000) for 5926 atoms. Found 14 (35 requested) and removed 25 (22 requested) atoms. Cycle 39: After refmac, R = 0.2049 (Rfree = 0.000) for 5911 atoms. Found 8 (35 requested) and removed 25 (22 requested) atoms. Cycle 40: After refmac, R = 0.2093 (Rfree = 0.000) for 5892 atoms. Found 14 (35 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6019 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6039 seeds are put forward Round 1: 388 peptides, 66 chains. Longest chain 21 peptides. Score 0.402 Round 2: 418 peptides, 59 chains. Longest chain 22 peptides. Score 0.499 Round 3: 415 peptides, 61 chains. Longest chain 23 peptides. Score 0.481 Round 4: 419 peptides, 56 chains. Longest chain 20 peptides. Score 0.521 Round 5: 408 peptides, 55 chains. Longest chain 18 peptides. Score 0.511 Taking the results from Round 4 Chains 58, Residues 363, Estimated correctness of the model 0.8 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 13293 restraints for refining 5963 atoms. 11790 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2161 (Rfree = 0.000) for 5963 atoms. Found 29 (36 requested) and removed 31 (22 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2073 (Rfree = 0.000) for 5948 atoms. Found 11 (36 requested) and removed 28 (22 requested) atoms. Cycle 43: After refmac, R = 0.2035 (Rfree = 0.000) for 5922 atoms. Found 10 (35 requested) and removed 24 (22 requested) atoms. Cycle 44: After refmac, R = 0.2101 (Rfree = 0.000) for 5903 atoms. Found 23 (35 requested) and removed 29 (22 requested) atoms. Cycle 45: After refmac, R = 0.2062 (Rfree = 0.000) for 5888 atoms. Found 16 (35 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6034 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6058 seeds are put forward Round 1: 325 peptides, 58 chains. Longest chain 14 peptides. Score 0.353 Round 2: 405 peptides, 58 chains. Longest chain 19 peptides. Score 0.486 Round 3: 388 peptides, 53 chains. Longest chain 22 peptides. Score 0.495 Round 4: 400 peptides, 55 chains. Longest chain 18 peptides. Score 0.499 Round 5: 384 peptides, 55 chains. Longest chain 19 peptides. Score 0.474 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 345, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 56 chains (345 residues) following loop building 2 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12971 reflections ( 99.85 % complete ) and 13576 restraints for refining 5965 atoms. 12194 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2161 (Rfree = 0.000) for 5965 atoms. Found 0 (36 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2077 (Rfree = 0.000) for 5929 atoms. Found 0 (35 requested) and removed 13 (22 requested) atoms. Cycle 48: After refmac, R = 0.2041 (Rfree = 0.000) for 5913 atoms. Found 0 (35 requested) and removed 3 (22 requested) atoms. Cycle 49: After refmac, R = 0.2146 (Rfree = 0.000) for 5903 atoms. TimeTaking 145.63