Mon 24 Dec 00:49:53 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 2nyh-1.7-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-1.7-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-1.7-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-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/2nyh-1.7-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-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 00:49:57 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/2nyh-1.7-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-1.7-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 293 and 0 Target number of residues in the AU: 293 Target solvent content: 0.4292 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 234 Adjusted target solvent content: 0.54 Input MTZ file: 2nyh-1.7-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: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-1.7-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1872 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 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 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: 55.335 1.699 Wilson plot Bfac: 11.46 30388 reflections ( 97.99 % complete ) and 0 restraints for refining 2083 atoms. Observations/parameters ratio is 3.65 ------------------------------------------------------ Starting model: R = 0.4009 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3781 (Rfree = 0.000) for 2083 atoms. Found 73 (113 requested) and removed 58 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.77 1.68 NCS extension: 0 residues added, 2098 seeds are put forward Round 1: 128 peptides, 25 chains. Longest chain 11 peptides. Score 0.346 Round 2: 137 peptides, 25 chains. Longest chain 13 peptides. Score 0.398 Round 3: 134 peptides, 25 chains. Longest chain 13 peptides. Score 0.381 Round 4: 128 peptides, 23 chains. Longest chain 14 peptides. Score 0.395 Round 5: 142 peptides, 24 chains. Longest chain 14 peptides. Score 0.449 Taking the results from Round 5 Chains 24, Residues 118, Estimated correctness of the model 85.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 3790 restraints for refining 1927 atoms. 3342 conditional restraints added. Observations/parameters ratio is 3.94 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3869 (Rfree = 0.000) for 1927 atoms. Found 105 (105 requested) and removed 37 (52 requested) atoms. Cycle 2: After refmac, R = 0.3654 (Rfree = 0.000) for 1994 atoms. Found 59 (108 requested) and removed 22 (54 requested) atoms. Cycle 3: After refmac, R = 0.3518 (Rfree = 0.000) for 2031 atoms. Found 58 (110 requested) and removed 9 (55 requested) atoms. Cycle 4: After refmac, R = 0.3371 (Rfree = 0.000) for 2080 atoms. Found 57 (113 requested) and removed 6 (56 requested) atoms. Cycle 5: After refmac, R = 0.3299 (Rfree = 0.000) for 2129 atoms. Found 55 (116 requested) and removed 1 (58 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.64 1.55 NCS extension: 3 residues added (0 deleted due to clashes), 2225 seeds are put forward Round 1: 109 peptides, 20 chains. Longest chain 12 peptides. Score 0.358 Round 2: 133 peptides, 19 chains. Longest chain 13 peptides. Score 0.515 Round 3: 131 peptides, 17 chains. Longest chain 14 peptides. Score 0.549 Round 4: 134 peptides, 18 chains. Longest chain 16 peptides. Score 0.542 Round 5: 139 peptides, 16 chains. Longest chain 16 peptides. Score 0.606 Taking the results from Round 5 Chains 16, Residues 123, Estimated correctness of the model 92.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 4218 restraints for refining 2104 atoms. 3742 conditional restraints added. Observations/parameters ratio is 3.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3507 (Rfree = 0.000) for 2104 atoms. Found 97 (114 requested) and removed 13 (57 requested) atoms. Cycle 7: After refmac, R = 0.3389 (Rfree = 0.000) for 2187 atoms. Found 63 (119 requested) and removed 10 (59 requested) atoms. Cycle 8: After refmac, R = 0.3290 (Rfree = 0.000) for 2239 atoms. Found 52 (122 requested) and removed 5 (61 requested) atoms. Cycle 9: After refmac, R = 0.3204 (Rfree = 0.000) for 2285 atoms. Found 43 (124 requested) and removed 5 (62 requested) atoms. Cycle 10: After refmac, R = 0.3129 (Rfree = 0.000) for 2320 atoms. Found 43 (126 requested) and removed 1 (63 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.63 1.55 NCS extension: 0 residues added, 2374 seeds are put forward Round 1: 129 peptides, 20 chains. Longest chain 14 peptides. Score 0.472 Round 2: 137 peptides, 17 chains. Longest chain 14 peptides. Score 0.577 Round 3: 146 peptides, 16 chains. Longest chain 25 peptides. Score 0.635 Round 4: 152 peptides, 20 chains. Longest chain 18 peptides. Score 0.583 Round 5: 143 peptides, 18 chains. Longest chain 26 peptides. Score 0.583 Taking the results from Round 3 Chains 17, Residues 130, Estimated correctness of the model 93.4 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 4592 restraints for refining 2314 atoms. 4037 conditional restraints added. Observations/parameters ratio is 3.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3334 (Rfree = 0.000) for 2314 atoms. Found 112 (126 requested) and removed 16 (63 requested) atoms. Cycle 12: After refmac, R = 0.3177 (Rfree = 0.000) for 2410 atoms. Found 61 (131 requested) and removed 4 (65 requested) atoms. Cycle 13: After refmac, R = 0.3094 (Rfree = 0.000) for 2467 atoms. Found 56 (134 requested) and removed 3 (67 requested) atoms. Cycle 14: After refmac, R = 0.3036 (Rfree = 0.000) for 2516 atoms. Found 70 (137 requested) and removed 7 (68 requested) atoms. Cycle 15: After refmac, R = 0.2975 (Rfree = 0.000) for 2577 atoms. Found 58 (140 requested) and removed 5 (70 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.60 1.52 NCS extension: 20 residues added (1 deleted due to clashes), 2655 seeds are put forward Round 1: 133 peptides, 19 chains. Longest chain 15 peptides. Score 0.515 Round 2: 140 peptides, 16 chains. Longest chain 20 peptides. Score 0.610 Round 3: 139 peptides, 15 chains. Longest chain 26 peptides. Score 0.625 Round 4: 136 peptides, 15 chains. Longest chain 26 peptides. Score 0.613 Round 5: 134 peptides, 15 chains. Longest chain 26 peptides. Score 0.604 Taking the results from Round 3 Chains 16, Residues 124, Estimated correctness of the model 93.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 5208 restraints for refining 2529 atoms. 4650 conditional restraints added. Observations/parameters ratio is 3.00 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3128 (Rfree = 0.000) for 2529 atoms. Found 106 (137 requested) and removed 27 (68 requested) atoms. Cycle 17: After refmac, R = 0.3002 (Rfree = 0.000) for 2608 atoms. Found 67 (142 requested) and removed 6 (71 requested) atoms. Cycle 18: After refmac, R = 0.2909 (Rfree = 0.000) for 2669 atoms. Found 41 (145 requested) and removed 3 (72 requested) atoms. Cycle 19: After refmac, R = 0.2849 (Rfree = 0.000) for 2707 atoms. Found 38 (147 requested) and removed 4 (73 requested) atoms. Cycle 20: After refmac, R = 0.2795 (Rfree = 0.000) for 2740 atoms. Found 30 (149 requested) and removed 0 (74 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.60 1.52 NCS extension: 20 residues added (1 deleted due to clashes), 2797 seeds are put forward Round 1: 128 peptides, 21 chains. Longest chain 13 peptides. Score 0.443 Round 2: 129 peptides, 15 chains. Longest chain 25 peptides. Score 0.582 Round 3: 123 peptides, 14 chains. Longest chain 25 peptides. Score 0.576 Round 4: 128 peptides, 14 chains. Longest chain 25 peptides. Score 0.598 Round 5: 124 peptides, 16 chains. Longest chain 17 peptides. Score 0.537 Taking the results from Round 4 Chains 16, Residues 114, Estimated correctness of the model 92.1 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 5738 restraints for refining 2672 atoms. 5239 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2969 (Rfree = 0.000) for 2672 atoms. Found 97 (145 requested) and removed 27 (72 requested) atoms. Cycle 22: After refmac, R = 0.2901 (Rfree = 0.000) for 2742 atoms. Found 60 (149 requested) and removed 0 (74 requested) atoms. Cycle 23: After refmac, R = 0.2822 (Rfree = 0.000) for 2802 atoms. Found 45 (152 requested) and removed 2 (76 requested) atoms. Cycle 24: After refmac, R = 0.2786 (Rfree = 0.000) for 2843 atoms. Found 38 (154 requested) and removed 0 (77 requested) atoms. Cycle 25: After refmac, R = 0.2729 (Rfree = 0.000) for 2881 atoms. Found 31 (156 requested) and removed 0 (78 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.59 1.51 NCS extension: 19 residues added (3 deleted due to clashes), 2937 seeds are put forward Round 1: 123 peptides, 15 chains. Longest chain 18 peptides. Score 0.554 Round 2: 125 peptides, 14 chains. Longest chain 17 peptides. Score 0.585 Round 3: 120 peptides, 14 chains. Longest chain 16 peptides. Score 0.562 Round 4: 125 peptides, 16 chains. Longest chain 15 peptides. Score 0.542 Round 5: 122 peptides, 14 chains. Longest chain 16 peptides. Score 0.571 Taking the results from Round 2 Chains 14, Residues 111, Estimated correctness of the model 91.6 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 6294 restraints for refining 2827 atoms. 5808 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2881 (Rfree = 0.000) for 2827 atoms. Found 102 (154 requested) and removed 18 (77 requested) atoms. Cycle 27: After refmac, R = 0.2837 (Rfree = 0.000) for 2910 atoms. Found 72 (158 requested) and removed 7 (79 requested) atoms. Cycle 28: After refmac, R = 0.2794 (Rfree = 0.000) for 2974 atoms. Found 51 (161 requested) and removed 5 (80 requested) atoms. Cycle 29: After refmac, R = 0.2753 (Rfree = 0.000) for 3017 atoms. Found 53 (164 requested) and removed 4 (82 requested) atoms. Cycle 30: After refmac, R = 0.2730 (Rfree = 0.000) for 3066 atoms. Found 36 (166 requested) and removed 2 (83 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.59 1.51 NCS extension: 5 residues added (0 deleted due to clashes), 3108 seeds are put forward Round 1: 125 peptides, 16 chains. Longest chain 17 peptides. Score 0.542 Round 2: 127 peptides, 14 chains. Longest chain 17 peptides. Score 0.594 Round 3: 126 peptides, 13 chains. Longest chain 18 peptides. Score 0.610 Round 4: 134 peptides, 15 chains. Longest chain 29 peptides. Score 0.604 Round 5: 129 peptides, 13 chains. Longest chain 25 peptides. Score 0.623 Taking the results from Round 5 Chains 14, Residues 116, Estimated correctness of the model 93.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 6778 restraints for refining 2966 atoms. 6283 conditional restraints added. Observations/parameters ratio is 2.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2897 (Rfree = 0.000) for 2966 atoms. Found 111 (161 requested) and removed 5 (80 requested) atoms. Cycle 32: After refmac, R = 0.2808 (Rfree = 0.000) for 3072 atoms. Found 72 (167 requested) and removed 4 (83 requested) atoms. Cycle 33: After refmac, R = 0.2746 (Rfree = 0.000) for 3138 atoms. Found 53 (171 requested) and removed 5 (85 requested) atoms. Cycle 34: After refmac, R = 0.2705 (Rfree = 0.000) for 3183 atoms. Found 69 (173 requested) and removed 5 (86 requested) atoms. Cycle 35: After refmac, R = 0.2680 (Rfree = 0.000) for 3246 atoms. Found 54 (176 requested) and removed 3 (88 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.57 1.49 NCS extension: 0 residues added, 3298 seeds are put forward Round 1: 113 peptides, 16 chains. Longest chain 15 peptides. Score 0.481 Round 2: 124 peptides, 12 chains. Longest chain 38 peptides. Score 0.622 Round 3: 122 peptides, 16 chains. Longest chain 14 peptides. Score 0.527 Round 4: 122 peptides, 14 chains. Longest chain 18 peptides. Score 0.571 Round 5: 111 peptides, 14 chains. Longest chain 13 peptides. Score 0.517 Taking the results from Round 2 Chains 13, Residues 112, Estimated correctness of the model 92.9 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 7099 restraints for refining 3170 atoms. 6518 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2812 (Rfree = 0.000) for 3170 atoms. Found 131 (172 requested) and removed 39 (86 requested) atoms. Cycle 37: After refmac, R = 0.2725 (Rfree = 0.000) for 3262 atoms. Found 55 (177 requested) and removed 10 (88 requested) atoms. Cycle 38: After refmac, R = 0.2664 (Rfree = 0.000) for 3304 atoms. Found 47 (180 requested) and removed 6 (90 requested) atoms. Cycle 39: After refmac, R = 0.2613 (Rfree = 0.000) for 3343 atoms. Found 50 (182 requested) and removed 2 (91 requested) atoms. Cycle 40: After refmac, R = 0.2559 (Rfree = 0.000) for 3385 atoms. Found 40 (184 requested) and removed 5 (92 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.59 1.51 NCS extension: 0 residues added, 3422 seeds are put forward Round 1: 122 peptides, 17 chains. Longest chain 19 peptides. Score 0.504 Round 2: 123 peptides, 15 chains. Longest chain 21 peptides. Score 0.554 Round 3: 119 peptides, 14 chains. Longest chain 21 peptides. Score 0.557 Round 4: 118 peptides, 16 chains. Longest chain 15 peptides. Score 0.507 Round 5: 122 peptides, 15 chains. Longest chain 16 peptides. Score 0.549 Taking the results from Round 3 Chains 14, Residues 105, Estimated correctness of the model 90.6 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 30388 reflections ( 97.99 % complete ) and 7500 restraints for refining 3254 atoms. 7000 conditional restraints added. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2784 (Rfree = 0.000) for 3254 atoms. Found 136 (177 requested) and removed 28 (88 requested) atoms. Cycle 42: After refmac, R = 0.2695 (Rfree = 0.000) for 3361 atoms. Found 75 (183 requested) and removed 7 (91 requested) atoms. Cycle 43: After refmac, R = 0.2603 (Rfree = 0.000) for 3428 atoms. Found 69 (186 requested) and removed 8 (93 requested) atoms. Cycle 44: After refmac, R = 0.2564 (Rfree = 0.000) for 3486 atoms. Found 56 (189 requested) and removed 5 (94 requested) atoms. Cycle 45: After refmac, R = 0.2540 (Rfree = 0.000) for 3535 atoms. Found 54 (192 requested) and removed 10 (96 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.56 1.48 NCS extension: 13 residues added (1 deleted due to clashes), 3593 seeds are put forward Round 1: 122 peptides, 19 chains. Longest chain 13 peptides. Score 0.458 Round 2: 122 peptides, 16 chains. Longest chain 21 peptides. Score 0.527 Round 3: 121 peptides, 18 chains. Longest chain 14 peptides. Score 0.476 Round 4: 115 peptides, 17 chains. Longest chain 14 peptides. Score 0.467 Round 5: 120 peptides, 18 chains. Longest chain 15 peptides. Score 0.471 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 106, Estimated correctness of the model 89.4 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2nyh-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 30388 reflections ( 97.99 % complete ) and 8162 restraints for refining 3375 atoms. 7754 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2647 (Rfree = 0.000) for 3375 atoms. Found 0 (184 requested) and removed 6 (92 requested) atoms. Cycle 47: After refmac, R = 0.2585 (Rfree = 0.000) for 3369 atoms. Found 0 (183 requested) and removed 1 (91 requested) atoms. Cycle 48: After refmac, R = 0.2561 (Rfree = 0.000) for 3368 atoms. Found 0 (183 requested) and removed 1 (91 requested) atoms. Cycle 49: After refmac, R = 0.2557 (Rfree = 0.000) for 3367 atoms. TimeTaking 36.08