Mon 24 Dec 00:07:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hq7-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hq7-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hq7-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:07:45 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-parrot-mrncs/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 199 and 0 Target number of residues in the AU: 199 Target solvent content: 0.6197 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-3.2-parrot-mrncs.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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2336 target number of atoms Had to go as low as 0.75 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: 89.671 3.200 Wilson plot Bfac: 61.20 4803 reflections ( 99.48 % complete ) and 0 restraints for refining 2594 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3051 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2426 (Rfree = 0.000) for 2594 atoms. Found 22 (23 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 2654 seeds are put forward NCS extension: 0 residues added, 2654 seeds are put forward Round 1: 141 peptides, 22 chains. Longest chain 13 peptides. Score 0.484 Round 2: 185 peptides, 22 chains. Longest chain 17 peptides. Score 0.673 Round 3: 196 peptides, 21 chains. Longest chain 24 peptides. Score 0.723 Round 4: 198 peptides, 18 chains. Longest chain 25 peptides. Score 0.768 Round 5: 207 peptides, 21 chains. Longest chain 29 peptides. Score 0.754 Taking the results from Round 4 Chains 20, Residues 180, Estimated correctness of the model 78.2 % 3 chains (57 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 102 A and 109 A 18 chains (185 residues) following loop building 2 chains (63 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 3838 restraints for refining 2133 atoms. 2855 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2638 (Rfree = 0.000) for 2133 atoms. Found 13 (19 requested) and removed 39 (9 requested) atoms. Cycle 2: After refmac, R = 0.2811 (Rfree = 0.000) for 2079 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 3: After refmac, R = 0.2751 (Rfree = 0.000) for 2062 atoms. Found 15 (17 requested) and removed 24 (9 requested) atoms. Cycle 4: After refmac, R = 0.2320 (Rfree = 0.000) for 2033 atoms. Found 12 (17 requested) and removed 13 (9 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2205 (Rfree = 0.000) for 2025 atoms. Found 6 (17 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 3.37 Search for helices and strands: 0 residues in 0 chains, 2099 seeds are put forward NCS extension: 31 residues added (17 deleted due to clashes), 2130 seeds are put forward Round 1: 186 peptides, 18 chains. Longest chain 26 peptides. Score 0.735 Round 2: 209 peptides, 18 chains. Longest chain 27 peptides. Score 0.795 Round 3: 209 peptides, 18 chains. Longest chain 25 peptides. Score 0.795 Round 4: 220 peptides, 19 chains. Longest chain 26 peptides. Score 0.808 Round 5: 224 peptides, 18 chains. Longest chain 28 peptides. Score 0.826 Taking the results from Round 5 Chains 23, Residues 206, Estimated correctness of the model 87.2 % 3 chains (37 residues) have been docked in sequence Building loops using Loopy2018 23 chains (206 residues) following loop building 3 chains (37 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4084 restraints for refining 2133 atoms. 3135 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2415 (Rfree = 0.000) for 2133 atoms. Found 17 (17 requested) and removed 19 (9 requested) atoms. Cycle 7: After refmac, R = 0.2126 (Rfree = 0.000) for 2125 atoms. Found 7 (17 requested) and removed 9 (9 requested) atoms. Cycle 8: After refmac, R = 0.2023 (Rfree = 0.000) for 2115 atoms. Found 6 (16 requested) and removed 9 (9 requested) atoms. Cycle 9: After refmac, R = 0.1968 (Rfree = 0.000) for 2109 atoms. Found 1 (15 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.1932 (Rfree = 0.000) for 2100 atoms. Found 3 (15 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2173 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 2192 seeds are put forward Round 1: 195 peptides, 19 chains. Longest chain 19 peptides. Score 0.748 Round 2: 207 peptides, 20 chains. Longest chain 27 peptides. Score 0.767 Round 3: 213 peptides, 21 chains. Longest chain 26 peptides. Score 0.770 Round 4: 221 peptides, 19 chains. Longest chain 35 peptides. Score 0.810 Round 5: 198 peptides, 20 chains. Longest chain 26 peptides. Score 0.743 Taking the results from Round 4 Chains 21, Residues 202, Estimated correctness of the model 84.9 % 4 chains (85 residues) have been docked in sequence Building loops using Loopy2018 21 chains (202 residues) following loop building 4 chains (85 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 3700 restraints for refining 2133 atoms. 2545 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2447 (Rfree = 0.000) for 2133 atoms. Found 15 (15 requested) and removed 20 (9 requested) atoms. Cycle 12: After refmac, R = 0.2233 (Rfree = 0.000) for 2117 atoms. Found 6 (15 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2167 (Rfree = 0.000) for 2106 atoms. Found 4 (14 requested) and removed 11 (9 requested) atoms. Cycle 14: After refmac, R = 0.2043 (Rfree = 0.000) for 2091 atoms. Found 13 (13 requested) and removed 12 (9 requested) atoms. Cycle 15: After refmac, R = 0.1918 (Rfree = 0.000) for 2084 atoms. Found 9 (13 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 2162 seeds are put forward NCS extension: 43 residues added (7 deleted due to clashes), 2205 seeds are put forward Round 1: 190 peptides, 20 chains. Longest chain 24 peptides. Score 0.719 Round 2: 193 peptides, 20 chains. Longest chain 26 peptides. Score 0.728 Round 3: 201 peptides, 19 chains. Longest chain 24 peptides. Score 0.764 Round 4: 209 peptides, 17 chains. Longest chain 30 peptides. Score 0.806 Round 5: 205 peptides, 20 chains. Longest chain 22 peptides. Score 0.762 Taking the results from Round 4 Chains 18, Residues 192, Estimated correctness of the model 84.3 % 3 chains (66 residues) have been docked in sequence Building loops using Loopy2018 18 chains (192 residues) following loop building 3 chains (66 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4008 restraints for refining 2133 atoms. 2984 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2333 (Rfree = 0.000) for 2133 atoms. Found 13 (13 requested) and removed 18 (9 requested) atoms. Cycle 17: After refmac, R = 0.2073 (Rfree = 0.000) for 2122 atoms. Found 5 (13 requested) and removed 9 (9 requested) atoms. Cycle 18: After refmac, R = 0.2020 (Rfree = 0.000) for 2115 atoms. Found 6 (12 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.1995 (Rfree = 0.000) for 2110 atoms. Found 6 (12 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2037 (Rfree = 0.000) for 2102 atoms. Found 4 (11 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.40 Search for helices and strands: 0 residues in 0 chains, 2161 seeds are put forward NCS extension: 26 residues added (20 deleted due to clashes), 2187 seeds are put forward Round 1: 183 peptides, 24 chains. Longest chain 13 peptides. Score 0.632 Round 2: 201 peptides, 18 chains. Longest chain 37 peptides. Score 0.776 Round 3: 196 peptides, 19 chains. Longest chain 25 peptides. Score 0.750 Round 4: 191 peptides, 14 chains. Longest chain 37 peptides. Score 0.799 Round 5: 193 peptides, 20 chains. Longest chain 36 peptides. Score 0.728 Taking the results from Round 4 Chains 15, Residues 177, Estimated correctness of the model 83.3 % 2 chains (61 residues) have been docked in sequence Building loops using Loopy2018 15 chains (177 residues) following loop building 2 chains (61 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4046 restraints for refining 2133 atoms. 3082 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2244 (Rfree = 0.000) for 2133 atoms. Found 11 (11 requested) and removed 19 (9 requested) atoms. Cycle 22: After refmac, R = 0.2061 (Rfree = 0.000) for 2119 atoms. Found 4 (11 requested) and removed 13 (9 requested) atoms. Cycle 23: After refmac, R = 0.1943 (Rfree = 0.000) for 2108 atoms. Found 5 (10 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.1890 (Rfree = 0.000) for 2100 atoms. Found 2 (10 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.1765 (Rfree = 0.000) for 2091 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2152 seeds are put forward NCS extension: 31 residues added (16 deleted due to clashes), 2183 seeds are put forward Round 1: 175 peptides, 22 chains. Longest chain 14 peptides. Score 0.636 Round 2: 198 peptides, 21 chains. Longest chain 28 peptides. Score 0.729 Round 3: 195 peptides, 20 chains. Longest chain 28 peptides. Score 0.734 Round 4: 188 peptides, 20 chains. Longest chain 37 peptides. Score 0.713 Round 5: 190 peptides, 18 chains. Longest chain 37 peptides. Score 0.747 Taking the results from Round 5 Chains 18, Residues 172, Estimated correctness of the model 74.5 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4230 restraints for refining 2133 atoms. 3384 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2183 (Rfree = 0.000) for 2133 atoms. Found 9 (9 requested) and removed 11 (9 requested) atoms. Cycle 27: After refmac, R = 0.1933 (Rfree = 0.000) for 2126 atoms. Found 6 (9 requested) and removed 14 (9 requested) atoms. Cycle 28: After refmac, R = 0.1907 (Rfree = 0.000) for 2113 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2140 (Rfree = 0.000) for 2107 atoms. Found 7 (9 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.1668 (Rfree = 0.000) for 2101 atoms. Found 7 (9 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 2166 seeds are put forward NCS extension: 39 residues added (8 deleted due to clashes), 2205 seeds are put forward Round 1: 170 peptides, 22 chains. Longest chain 17 peptides. Score 0.616 Round 2: 172 peptides, 17 chains. Longest chain 26 peptides. Score 0.707 Round 3: 178 peptides, 19 chains. Longest chain 29 peptides. Score 0.696 Round 4: 176 peptides, 20 chains. Longest chain 26 peptides. Score 0.673 Round 5: 181 peptides, 18 chains. Longest chain 31 peptides. Score 0.720 Taking the results from Round 5 Chains 18, Residues 163, Estimated correctness of the model 69.3 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4331 restraints for refining 2133 atoms. 3549 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1946 (Rfree = 0.000) for 2133 atoms. Found 9 (9 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.1790 (Rfree = 0.000) for 2126 atoms. Found 6 (9 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.1773 (Rfree = 0.000) for 2118 atoms. Found 9 (9 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.1700 (Rfree = 0.000) for 2114 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.1731 (Rfree = 0.000) for 2105 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 2145 seeds are put forward NCS extension: 36 residues added (8 deleted due to clashes), 2181 seeds are put forward Round 1: 161 peptides, 24 chains. Longest chain 16 peptides. Score 0.539 Round 2: 191 peptides, 24 chains. Longest chain 22 peptides. Score 0.662 Round 3: 176 peptides, 19 chains. Longest chain 24 peptides. Score 0.689 Round 4: 167 peptides, 16 chains. Longest chain 22 peptides. Score 0.706 Round 5: 171 peptides, 21 chains. Longest chain 22 peptides. Score 0.638 Taking the results from Round 4 Chains 16, Residues 151, Estimated correctness of the model 66.4 % 2 chains (41 residues) have been docked in sequence Building loops using Loopy2018 16 chains (151 residues) following loop building 2 chains (41 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4215 restraints for refining 2132 atoms. 3438 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2011 (Rfree = 0.000) for 2132 atoms. Found 9 (9 requested) and removed 13 (9 requested) atoms. Cycle 37: After refmac, R = 0.2316 (Rfree = 0.000) for 2124 atoms. Found 9 (9 requested) and removed 13 (9 requested) atoms. Cycle 38: After refmac, R = 0.1874 (Rfree = 0.000) for 2117 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1727 (Rfree = 0.000) for 2109 atoms. Found 6 (9 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.1610 (Rfree = 0.000) for 2103 atoms. Found 1 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 2179 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2195 seeds are put forward Round 1: 135 peptides, 18 chains. Longest chain 19 peptides. Score 0.541 Round 2: 156 peptides, 19 chains. Longest chain 23 peptides. Score 0.614 Round 3: 151 peptides, 20 chains. Longest chain 21 peptides. Score 0.574 Round 4: 145 peptides, 16 chains. Longest chain 21 peptides. Score 0.625 Round 5: 141 peptides, 15 chains. Longest chain 21 peptides. Score 0.628 Taking the results from Round 5 Chains 15, Residues 126, Estimated correctness of the model 48.4 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4439 restraints for refining 2133 atoms. 3803 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1900 (Rfree = 0.000) for 2133 atoms. Found 9 (9 requested) and removed 14 (9 requested) atoms. Cycle 42: After refmac, R = 0.1732 (Rfree = 0.000) for 2125 atoms. Found 5 (9 requested) and removed 10 (9 requested) atoms. Cycle 43: After refmac, R = 0.2138 (Rfree = 0.000) for 2119 atoms. Found 9 (9 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.1580 (Rfree = 0.000) for 2116 atoms. Found 2 (9 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.1786 (Rfree = 0.000) for 2106 atoms. Found 9 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 2159 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 2181 seeds are put forward Round 1: 144 peptides, 22 chains. Longest chain 15 peptides. Score 0.499 Round 2: 164 peptides, 24 chains. Longest chain 15 peptides. Score 0.553 Round 3: 167 peptides, 24 chains. Longest chain 14 peptides. Score 0.566 Round 4: 175 peptides, 25 chains. Longest chain 15 peptides. Score 0.582 Round 5: 168 peptides, 24 chains. Longest chain 15 peptides. Score 0.571 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 150, Estimated correctness of the model 36.1 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hq7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4803 reflections ( 99.48 % complete ) and 4730 restraints for refining 2133 atoms. 4155 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1801 (Rfree = 0.000) for 2133 atoms. Found 0 (9 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1712 (Rfree = 0.000) for 2122 atoms. Found 0 (9 requested) and removed 7 (9 requested) atoms. Cycle 48: After refmac, R = 0.2070 (Rfree = 0.000) for 2114 atoms. Found 0 (9 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1699 (Rfree = 0.000) for 2102 atoms. TimeTaking 27.73