Sun 23 Dec 22:22:40 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 1vmg-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-1.5-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/1vmg-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-1.5-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 22:22:49 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/1vmg-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-1.5-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 155 and 0 Target number of residues in the AU: 155 Target solvent content: 0.4499 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 2 Adjusted target number of residues: 190 Adjusted target solvent content: 0.33 Input MTZ file: 1vmg-1.5-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: 98 Cell parameters: 79.748 79.748 95.906 90.000 90.000 90.000 Input sequence file: 1vmg-1.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.35 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 Loops will be built when appropriate and at the last cycle Resolution range: 61.319 1.460 Wilson plot Bfac: 14.18 25370 reflections ( 93.40 % complete ) and 0 restraints for refining 3057 atoms. Observations/parameters ratio is 2.07 ------------------------------------------------------ Starting model: R = 0.3531 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2975 (Rfree = 0.000) for 3057 atoms. Found 51 (256 requested) and removed 351 (128 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.66 2.10 Round 1: 80 peptides, 2 chains. Longest chain 47 peptides. Score 0.828 Round 2: 81 peptides, 2 chains. Longest chain 42 peptides. Score 0.832 Round 3: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 25370 reflections ( 93.40 % complete ) and 2309 restraints for refining 1556 atoms. 1646 conditional restraints added. Observations/parameters ratio is 4.08 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3115 (Rfree = 0.000) for 1556 atoms. Found 44 (130 requested) and removed 83 (65 requested) atoms. Cycle 2: After refmac, R = 0.2824 (Rfree = 0.000) for 1506 atoms. Found 34 (124 requested) and removed 65 (63 requested) atoms. Cycle 3: After refmac, R = 0.2547 (Rfree = 0.000) for 1466 atoms. Found 24 (118 requested) and removed 62 (61 requested) atoms. Cycle 4: After refmac, R = 0.2394 (Rfree = 0.000) for 1420 atoms. Found 24 (112 requested) and removed 59 (59 requested) atoms. Cycle 5: After refmac, R = 0.2271 (Rfree = 0.000) for 1379 atoms. Found 32 (107 requested) and removed 58 (58 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.52 1.92 Round 1: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Round 2: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 3: 81 peptides, 3 chains. Longest chain 36 peptides. Score 0.808 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 81 peptides, 4 chains. Longest chain 36 peptides. Score 0.783 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 25370 reflections ( 93.40 % complete ) and 1848 restraints for refining 1282 atoms. 1185 conditional restraints added. Observations/parameters ratio is 4.95 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2145 (Rfree = 0.000) for 1282 atoms. Found 42 (96 requested) and removed 53 (53 requested) atoms. Cycle 7: After refmac, R = 0.2055 (Rfree = 0.000) for 1266 atoms. Found 34 (93 requested) and removed 53 (53 requested) atoms. Cycle 8: After refmac, R = 0.2034 (Rfree = 0.000) for 1235 atoms. Found 43 (89 requested) and removed 52 (52 requested) atoms. Cycle 9: After refmac, R = 0.2040 (Rfree = 0.000) for 1221 atoms. Found 35 (86 requested) and removed 52 (51 requested) atoms. Cycle 10: After refmac, R = 0.2024 (Rfree = 0.000) for 1189 atoms. Found 47 (82 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.51 1.91 Round 1: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Round 2: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 3: 80 peptides, 3 chains. Longest chain 42 peptides. Score 0.804 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 25370 reflections ( 93.40 % complete ) and 1512 restraints for refining 1113 atoms. 849 conditional restraints added. Observations/parameters ratio is 5.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2112 (Rfree = 0.000) for 1113 atoms. Found 46 (74 requested) and removed 47 (46 requested) atoms. Cycle 12: After refmac, R = 0.2024 (Rfree = 0.000) for 1104 atoms. Found 52 (73 requested) and removed 47 (46 requested) atoms. Cycle 13: After refmac, R = 0.1994 (Rfree = 0.000) for 1095 atoms. Found 55 (70 requested) and removed 46 (46 requested) atoms. Cycle 14: After refmac, R = 0.2029 (Rfree = 0.000) for 1094 atoms. Found 45 (68 requested) and removed 42 (46 requested) atoms. Cycle 15: After refmac, R = 0.2039 (Rfree = 0.000) for 1073 atoms. Found 48 (66 requested) and removed 29 (45 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.51 1.91 Round 1: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Round 2: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 3: 80 peptides, 3 chains. Longest chain 42 peptides. Score 0.804 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 25370 reflections ( 93.40 % complete ) and 1283 restraints for refining 1026 atoms. 620 conditional restraints added. Observations/parameters ratio is 6.18 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2097 (Rfree = 0.000) for 1026 atoms. Found 53 (60 requested) and removed 39 (43 requested) atoms. Cycle 17: After refmac, R = 0.2024 (Rfree = 0.000) for 1036 atoms. Found 39 (59 requested) and removed 28 (43 requested) atoms. Cycle 18: After refmac, R = 0.1966 (Rfree = 0.000) for 1036 atoms. Found 55 (57 requested) and removed 21 (43 requested) atoms. Cycle 19: After refmac, R = 0.1969 (Rfree = 0.000) for 1064 atoms. Found 45 (59 requested) and removed 36 (44 requested) atoms. Cycle 20: After refmac, R = 0.1936 (Rfree = 0.000) for 1059 atoms. Found 57 (57 requested) and removed 30 (44 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.51 1.91 Round 1: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Round 2: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 3: 80 peptides, 3 chains. Longest chain 42 peptides. Score 0.804 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 25370 reflections ( 93.40 % complete ) and 1293 restraints for refining 1021 atoms. 630 conditional restraints added. Observations/parameters ratio is 6.21 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2241 (Rfree = 0.000) for 1021 atoms. Found 44 (53 requested) and removed 30 (42 requested) atoms. Cycle 22: After refmac, R = 0.2007 (Rfree = 0.000) for 1031 atoms. Found 33 (52 requested) and removed 14 (43 requested) atoms. Cycle 23: After refmac, R = 0.1940 (Rfree = 0.000) for 1036 atoms. Found 48 (52 requested) and removed 18 (43 requested) atoms. Cycle 24: After refmac, R = 0.1912 (Rfree = 0.000) for 1059 atoms. Found 44 (53 requested) and removed 24 (44 requested) atoms. Cycle 25: After refmac, R = 0.1924 (Rfree = 0.000) for 1065 atoms. Found 35 (52 requested) and removed 28 (45 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.51 1.91 Round 1: 79 peptides, 2 chains. Longest chain 48 peptides. Score 0.824 Round 2: 79 peptides, 2 chains. Longest chain 41 peptides. Score 0.824 Round 3: 79 peptides, 2 chains. Longest chain 48 peptides. Score 0.824 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 79 peptides, 2 chains. Longest chain 48 peptides. Score 0.824 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 25370 reflections ( 93.40 % complete ) and 1274 restraints for refining 1007 atoms. 611 conditional restraints added. Observations/parameters ratio is 6.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2000 (Rfree = 0.000) for 1007 atoms. Found 47 (47 requested) and removed 20 (42 requested) atoms. Cycle 27: After refmac, R = 0.1951 (Rfree = 0.000) for 1027 atoms. Found 42 (48 requested) and removed 11 (43 requested) atoms. Cycle 28: After refmac, R = 0.1935 (Rfree = 0.000) for 1044 atoms. Found 35 (49 requested) and removed 21 (44 requested) atoms. Cycle 29: After refmac, R = 0.1896 (Rfree = 0.000) for 1053 atoms. Found 32 (48 requested) and removed 22 (44 requested) atoms. Cycle 30: After refmac, R = 0.1875 (Rfree = 0.000) for 1044 atoms. Found 43 (46 requested) and removed 14 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.51 1.91 Round 1: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Round 2: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 3: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 25370 reflections ( 93.40 % complete ) and 1278 restraints for refining 1013 atoms. 615 conditional restraints added. Observations/parameters ratio is 6.26 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2196 (Rfree = 0.000) for 1013 atoms. Found 41 (44 requested) and removed 18 (42 requested) atoms. Cycle 32: After refmac, R = 0.1995 (Rfree = 0.000) for 1034 atoms. Found 35 (45 requested) and removed 11 (43 requested) atoms. Cycle 33: After refmac, R = 0.1967 (Rfree = 0.000) for 1050 atoms. Found 39 (46 requested) and removed 20 (44 requested) atoms. Cycle 34: After refmac, R = 0.1940 (Rfree = 0.000) for 1051 atoms. Found 44 (44 requested) and removed 13 (44 requested) atoms. Cycle 35: After refmac, R = 0.1944 (Rfree = 0.000) for 1069 atoms. Found 42 (45 requested) and removed 19 (45 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.51 1.91 Round 1: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Round 2: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 3: 80 peptides, 3 chains. Longest chain 42 peptides. Score 0.804 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 25370 reflections ( 93.40 % complete ) and 1282 restraints for refining 1023 atoms. 619 conditional restraints added. Observations/parameters ratio is 6.20 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2188 (Rfree = 0.000) for 1023 atoms. Found 42 (42 requested) and removed 23 (42 requested) atoms. Cycle 37: After refmac, R = 0.1999 (Rfree = 0.000) for 1037 atoms. Found 41 (43 requested) and removed 17 (43 requested) atoms. Cycle 38: After refmac, R = 0.1942 (Rfree = 0.000) for 1053 atoms. Found 43 (44 requested) and removed 11 (44 requested) atoms. Cycle 39: After refmac, R = 0.1905 (Rfree = 0.000) for 1067 atoms. Found 40 (45 requested) and removed 24 (45 requested) atoms. Cycle 40: After refmac, R = 0.1894 (Rfree = 0.000) for 1064 atoms. Found 39 (45 requested) and removed 18 (45 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.51 1.91 Round 1: 79 peptides, 2 chains. Longest chain 48 peptides. Score 0.824 Round 2: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 3: 80 peptides, 3 chains. Longest chain 42 peptides. Score 0.804 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 79 peptides, 2 chains. Longest chain 48 peptides. Score 0.824 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 25370 reflections ( 93.40 % complete ) and 1267 restraints for refining 1011 atoms. 604 conditional restraints added. Observations/parameters ratio is 6.27 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2201 (Rfree = 0.000) for 1011 atoms. Found 42 (42 requested) and removed 25 (42 requested) atoms. Cycle 42: After refmac, R = 0.2035 (Rfree = 0.000) for 1026 atoms. Found 43 (43 requested) and removed 13 (43 requested) atoms. Cycle 43: After refmac, R = 0.1988 (Rfree = 0.000) for 1048 atoms. Found 39 (44 requested) and removed 19 (44 requested) atoms. Cycle 44: After refmac, R = 0.1987 (Rfree = 0.000) for 1055 atoms. Found 40 (44 requested) and removed 12 (44 requested) atoms. Cycle 45: After refmac, R = 0.1966 (Rfree = 0.000) for 1066 atoms. Found 39 (45 requested) and removed 25 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.51 1.91 Round 1: 81 peptides, 2 chains. Longest chain 49 peptides. Score 0.832 Round 2: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 3: 80 peptides, 3 chains. Longest chain 42 peptides. Score 0.804 Round 4: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.859 Round 5: 80 peptides, 3 chains. Longest chain 35 peptides. Score 0.804 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 99.3 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vmg-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 25370 reflections ( 93.40 % complete ) and 1246 restraints for refining 1015 atoms. 583 conditional restraints added. Observations/parameters ratio is 6.25 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2035 (Rfree = 0.000) for 1015 atoms. Found 0 (42 requested) and removed 1 (42 requested) atoms. Cycle 47: After refmac, R = 0.1886 (Rfree = 0.000) for 1007 atoms. Found 0 (42 requested) and removed 2 (42 requested) atoms. Cycle 48: After refmac, R = 0.1808 (Rfree = 0.000) for 1001 atoms. Found 0 (42 requested) and removed 0 (42 requested) atoms. Cycle 49: After refmac, R = 0.1776 (Rfree = 0.000) for 998 atoms. TimeTaking 29.28